Embassy charge d'affaires David Rank was a 27-year veteran State Department officer appointed to serve in Beijing in January last year.
"Mr Rank made a personal decision. We appreciate his years of dedicated service to the State Department," US embassy spokeswoman Mary Beth Polley told AFP.
Polley said the embassy informed China's foreign affairs ministry on Monday that Jonathan Fritz would be serving as charge d'affaires.
She declined to comment on when a permanent replacement for Rank would be announced.
Trump's choice as the new ambassador to China, former Iowa governor Terry Branstad, has yet to arrive in the country.
News of Rank's resignation was broken on Twitter by veteran China reporter John Pomfret, an editor at the SupChina news site, formerly of the Washington Post.
According to Pomfret, Rank stepped down because he "could not back Trump on climate" and had been dismayed by the president's decision to pull out of the Paris climate accord.
Pomfret added Rank had "called a town hall meeting" at the embassy "to say he could not deliver a demarche (initiative)" to China over US withdrawal from the Paris agreement.
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