The long-awaited probe comes after months of negotiations between the WHO and Beijing.
A group of 10 scientists is set to interview people from research institutes, hospitals and the seafood market linked to the initial outbreak.
Covid-19 was first detected in Wuhan in central China in late 2019.
The team's arrival on Thursday morning coincides with a resurgence of new coronavirus cases in the north of the country, while life in Wuhan is relatively back to normal.
They will undergo two weeks of quarantine before beginning their research, which will rely upon samples and evidence provided by Chinese officials.
Team leader Peter Ben Embarek told AFP news agency just before the trip that it "could be a very long journey before we get a full understanding of what happened".
"I don't think we will have clear answers after this initial mission, but we will be on the way," he said.