The Shanghai composite was down by 0.23 percent to close at around 2,645.43 while the Shenzhen composite ended its trading day just below flat at about 1,385.84.
Meanwhile, Hong Kong's Hang Seng index was higher by 0.4 percent during the final hour of trade.
China's markets have been closely watched by investors as a result of the ongoing trade spat between Beijing and Washington, with an anticipated meeting between Presidents Xi Jinping and Donald Trump at the upcoming G-20 meeting in Buenos Aires from Nov. 30 to Dec. 1.
One analyst told CNBC's "Street Signs" on Thursday that he is "not too hopeful" about next week's meeting.
"Both sides seem to be incredibly confused," said Andrew Collier, managing director at Orient Capital Research.
On the U.S. side, Collier said: "In the past couple of weeks you've had a situation where (Larry) Kudlow and (Peter) Navarro, the two economics gurus in D.C. are fighting with each other openly."
While in China, he added, former top trade negotiator Long Yongtu "made some nasty comments about the Chinese negotiating style" — something that was "kind of startling" given Long's former position as a senior official, Collier said.
Rest of Asia mostly sees gains
Japan's Nikkei 225 saw gains of 0.65 percent to close at 21,646.55 while the Topix advanced 0.81 percent to end its trading day at 1,628.96.
Shares of Japan's largest bank, Mitsubishi UFJ Financial Group, fell 1.43 percent after the New York Times reported that U.S. prosecutors are said to be investigating the lender's systems to track money laundering.
The moves in Tokyo came after Japan's core consumer prices saw a gain of 1.0 percent on a year-on-year basis, in line with expectations from economists surveyed in a Reuters poll.
In Australia, the benchmark ASX 200 rose 0.86 percent to close at 5,691.30, with most sectors seeing gains.
The heavily weighted financial subindex advanced 0.77 percent, with shares of Australia's so-called Big Four banks seeing gains. Australia and New Zealand Banking Group rose 1.3 percent, Commonwealth Bank of Australia gained 0.81 percent, National Australia Bank advanced 0.92 percent and Westpac was higher by 0.35 percent.
Meanwhile, South Korea's Kospi slipped 0.32 percent to close at 2,069.95.
Muted movements on Wall Street
To be sure, Wednesday's moves came on a day with very low trading volume as most of Wall Street was away for the Thanksgiving holiday. The SPDR S&P 500 ETF Trust (SPY), which tracks the S&P 500, traded just over 71 million shares, well below its 30-day average volume of 130.3 million.
"Markets experienced a better night last night, but it is fair to say that sentiment remains fragile," Daniel Gradwell from ANZ Research wrote in a morning note. "There seems a greater appreciation that with the impact of US fiscal stimulus waning, the US economy could slow like other major economies have. That leaves the market less forgiving of poor news."
Volatility is expected to persist unless there's a turnaround in global growth prospects, Gradwell added.
Oil prices slip after a partial recovery
The global benchmark Brent crude futures was up 81 cents, or 1.3 percent, at $63.34 per barrel at 2:30 p.m. ET Wednesday. Brent fell to a low going back to December 2017 in the previous session.
U.S. West Texas Intermediate crude ended Wednesday's session $1.20, or 2.3 percent higher, at $54.63. WTI hit its lowest price level since October 2017 on Tuesday.
Sentiment appeared to take a turn for the worse once again on Thursday afternoon in Asia. U.S. crude futures slipped 0.11 percent at $54.57 per barrel while Brent declined 0.11 percent at $63.41 per barrel.
U.S. crude stocks rose 4.9 million barrels last week, the Energy Information Administration said, a larger-than-expected increase. Crude inventories have risen for nine straight weeks, the longest streak of increases since March 2017.
Oil-related stocks in Asia were mixed on the back of Thursday's slip in crude prices.
Australia's Origin Energy gained 2.41 percent, Woodside Petroleum advanced 0.66 percent and Santos rose 1.05 percent.
In Japan, shares of JXTG rose 2.22 percent while Fuji Oil jumped more than 7 percent. Japan Petroleum Exploration, on the other hand, slipped by 0.73 percent and Inpex was lower by 2.55 percent.
Over in South Korea, S-Oil fell 0.45 percent while SK Innovation rose 0.98 percent.
China's oil sector was also hit to a certain extent, with China Petroleum & Chemical, also known as Sinopec, slipping 0.67 percent and China Oilfield Services declining by 0.11 percent. Petrochina, however, rose 0.26 percent.
Vishnu Varathan, head of economics and strategy at Mizuho Bank, said in a note that the current geopolitical situation between the U.S. and Saudi Arabia is "the cat among the pigeons for the Oil market," in reference to the ongoing dispute between the two countries over the killing of journalist Jamal Khashoggi.
"That inherently means that oil-induced volatility very much remains on the table," he said.
The Japanese yen was at 113.06 against the dollar after weakening from around the 112.7 handle yesterday. The Australian dollar traded at $0.7249 after rising from levels around $0.72 in the previous session.
— Reuters and CNBC's Fred Imbert contributed to this report.
European stocks close lower as investor sentiment remains cautious
By the end of trade, the pan-European Stoxx 600 was down 0.65 percent, with all major country indexes in negative territory.
Looking at individual stocks, Centrica finished down 9.02 percent. This after the owner of British Gas lost 372,000 home energy accounts in four months amid rising competition.
The board of Japanese auto giant Nissan has voted to remove Carlos Ghosn from the role of Chairman and Representative Director.
Nissan said on its website Monday that it will now form an advisory committee to propose nominations from the board of directors for Ghosn's replacement. A separate committee to review Nissan's governance and executive pay is also to be created.
Brexit progress continues to dominate European headlines on Thursday. Sterling jumped 1.2 percent after Britain and EU political leaders agreed in principle to a text setting out their future relationship. European Commission President Jean-Claude Juncker said Thursday, "The Commission president has informed me that it has been agreed at negotiators' level and agreed in principle at political level, subject to the endorsement of the leaders."
May said progress was being made on a draft agreement on future EU-U.K. relations (a separate agreement from the Brexit deal) but Spain has threatened to vote against the draft Brexit deal if it is left out of talks on the future status of Gibraltar, a British territory on Spain's southern coast. There is a meeting of EU leaders on Sunday at which they are expected to endorse the draft Brexit deal.
U.K. opposition Labour Party leader Jeremy Corbyn said in the House of Commons on Thursday that he deal was the "worst of all worlds."
His comments came soon after the publication of the political declaration on the framework for the U.K.'s future relations with the European Union.
Meanwhile, Italy's budget continues to cause a headache for Europe too. With Italy refusing to budge on its big spending plans for 2019, the European Commission announced on Wednesday that it is starting disciplinary measures against Italy which could result in it being fined. Investors are also keeping an eye on global trade developments.
Italian banks fell after Deputy Prime Minister Matteo Salvini said the government would not backtrack on its expansionary 2019 budget law following a rejection by the EU Commission.
Oil prices dipped on Thursday after U.S. crude inventories increased to their highest level since December 2017, fueling more concerns of a possible oversupply in markets.
U.S. financial markets are closed on Thursday for the Thanksgiving public holiday and there are no major earnings Thursday. Data releases include preliminary euro area consumer confidence numbers for November.