The airport said operations were seriously affected and the situation will likely continue as a thunderstorm is expected this evening. There were 234 arrivals and 181 departures as of 11 am.
Beijing weather authorities have raised their alert level to "orange" from "yellow" early by the afternoon, warning against lightning, hail, wind and as much as 70 mm (three inches) of rain, threatening flash floods in mountainous areas.
By early afternoon rain subsided in some parts of the capital, but nine roads were still flooded and 171 tourist sites were shut, the official news agency Xinhua said.
Torrential rainstorms are fairly frequent in Beijing in the summer months, often causing long delays at the airport.
Heavy rain was expected across south-eastern China on Saturday, it said.
Other airports affected by the downpours included Shanghai, Nanjing in Jiangsu province, Hangzhou in Zhejiang along the Yangtze River delta.
Widespread flooding hit two areas, Xiangbei and Xiangxi in the southern province of Hunan, Xinhua said. Rainfall across the province ranged from 100 mm (4 inches) to 200 mm (8 inches).
The extreme weather followed a tornado that struck Inner Mongolia on Friday, killing five people, injuring more than 50 and destroying homes in a major city.
More than 400 flights were cancelled yesterday.
(with inputs from Reuters and PTI)