A tornado smashed through the town of Dafeng, in Jiangsu province, killing three people, the official newspaper China Daily reported.
A total of 27 people were reported dead in Jiangsu, west of Shanghai, and about 40,000 were evacuated, Li Qiubao, an official of the Jiangsu Civil Affairs Bureau, said in a phone interview.
Newspapers showed residents using makeshift rafts to ferry through streets flooded chest-high.
In total, more than 13 million people were affected by the storms, reports said.
From June 21-July 5, Jiangsu had four times the usual amount of rainfall, the official Xinhua News Agency reported, citing provincial meteorological officials. Weather forecasts were for continued heavy rains.
In neighboring Anhui province, another three people were killed, said an official at the local Civil Affairs Bureau. Like many Chinese bureaucrats, he refused to give his name, the AP reports.
More than 40,000 people were displaced along the flood-prone Huai River, he said.
China suffers hundreds of rain deaths every summer. The impact of flooding has been worsened by heavy farming and tree-cutting that left cleared hillsides unable to trap rain. Major cities are shielded by flood dikes but small towns, especially in mountainous areas, are vulnerable to deadly flash floods.