State media said nearly 1,000 flights at Beijing Capital International Airport were grounded on Thursday while more than 500 were cancelled at Beijing's new Daxing International Airport.
Dozens of new Covid-19 cases have been recorded in the past few days with most tied to the sprawling Xinfadi wholesale market, Travel Mole reported.
The market has recorded more than 130 cases in the past week.
City officials have urged residents not to leave Beijing.
"Because the Xinfadi market is the largest marketplace selling daily necessities, with thousands of migrant workers and a large number of visitors, it is hard to control the spread," said Pang Xinghuo, deputy director of the Beijing Center for Disease Control and Prevention.
"We may see a rise in confirmed cases in the coming days."
Officials are ramping up testing with thousands of people being tested every day.