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.