Foreign ministry spokesman Zhao Lijian said the move was "another demonstration of the US pursuing unilateralism, withdrawing from groups and breaking contracts".
WHO is "the most authoritative and professional international institution in the field of global public health security", Mr Zhao said, adding that the US departure would particularly hurt developing countries in need of international support.
Mr Trump has criticised the WHO over its response to the coronavirus pandemic and accused it of bowing to Chinese influence.
He has claimed Chinese officials "ignored" their reporting obligations to WHO and pressured the organisation to mislead the public about an outbreak that has now killed more than 130,000 Americans.
WHO plans to send a team to China to investigate the source of the virus, which was first detected in the central city of Wuhan last year.
China has said it remains unclear where the virus originated and has rejected an independent probe, but reiterated this week that it is working closely with WHO and will "continue to support scientists from all countries to carry out global scientific research on the source and spread of viruses".
The Trump administration formally notified the UN on Monday of its withdrawal from WHO, although the decision will not take effect until July 6 next year, which means it could be reversed by a new administration or if circumstances change.
Former Vice President Joe Biden, the presumptive Democratic presidential nominee, said he would reverse the decision on his first day in office if elected.
Health officials and critics of Trump’s administration say the withdrawal would cost the US influence in the global arena while undermining an important institution which is leading vaccine development efforts and drug trials to address the coronavirus.
Additional reporting from the Associated Press