The storm, which started Saturday afternoon, flooded major roads and sent torrents of water tumbling down steps.
In Tongzhou, a Beijing suburb, two people died when a roof collapsed and another was killed after being struck by lightning, the state-run Xinhua news agency reported Sunday.
The other deaths were caused by electric shocks from downed power lines and drowning, the report added.
More than 500 flights were cancelled at Beijing's Capital International Airport, according to the Beijing News.
On average around 170 millimetres (6.7 inches) of rain fell, though a township west of Beijing was hit by 460 millimetres (18.1 inches), Xinhua added.