He said the WHO had "failed in its basic duty" in its response to the coronavirus outbreak.
He accused the UN body of mismanaging and covering up the spread of the virus after it emerged in China, and said it must be held accountable.
Mr Trump has previously accused the WHO of being biased towards China.
The US president has himself come under criticism at home over his handling of the outbreak.
"I am directing my administration to halt funding while a review is conducted to assess the World Health Organization's role in severely mismanaging and covering up the spread of the coronavirus," Mr Trump told a news conference at the White House.
Reacting to Mr Trump's remarks, UN Secretary-General António Guterres said now was "not the time" to be cutting resources for the WHO.
The US is the WHO's biggest single funder, providing $400m (£316m) last year - just under 15% of its total budget.