Austin Ramzy, who has been based in China for more than six years, departed Beijing for Taipei, where he will be based.
"China is forcing out Austin Ramzy today after 6.5 years," Times China correspondent Ed Wong wrote on Twitter.
"And we're off. Next stop, Taipei," Ramzy tweeted. In an earlier message, he wrote: "Sad to be leaving Beijing. Hope I can return soon."
His departure comes a month after US Vice President Joe Biden raised the issue of China's treatment of foreign journalists privately with Chinese leaders during a visit to Beijing.
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Authorities also reportedly conducted unannounced "inspections" of Bloomberg's bureaux in Beijing and Shanghai last month and demanded an apology from its editor-in-chief amid a controversy over an unpublished article on the government ties of a Chinese billionaire.
China's foreign ministry this week said that Ramzy's journalist visa, which the newspaper applied for in June after he joined from Time magazine, would not be ready before the end of the month, effectively obliging him to leave.
He is the third New York Times journalist to not be authorised to stay in China in 18 months, it pointed out in a statement.
"In these circumstances it is difficult to avoid the conclusion that the authorities are punishing the New York Times for articles it published concerning Premier Wen Jiabao and his family.