The National Meteorological Center raised the weather alert to yellow Sunday morning, the third-highest of four warning levels, for more than a half-dozen provinces and the cities of Shanghai and Chongqing.
Heavy to torrential rains were forecast into Monday afternoon.
Footage on state broadcaster CCTV showed flooded streets and farmland in Anhui province.
To the south in Jiangxi province, more than 8,000 people have been evacuated and 54 houses collapsed after rainstorms in recent days, the network said.
Nationwide, flooding-related disasters have destroyed 17,000 homes, caused $5.9 billion in economic losses and left 121 people dead or missing so far this year, the official People's Daily newspaper said in a social media post, citing the Ministry of Emergency Management.
The National Meteorological Center said some parts of Anhui, Hubei, Hunan and Zhejiang provinces could see 4 to 9 inches of rain. It also issued a yellow alert for rain in two northeastern provinces, Heilongjiang and Jilin.