The worst hit by the rains, which were followed by hail storms, was Guangdong province, the official Xinhua News Agency reported quoting sources in the Ministry of Civil Affairs and the National Committee for Disaster Reduction.
The province in the southernmost tip of mainland China is adjacent to Hong Kong and Macau and is the southern gateway to the country.
The ministry has sent work teams to Guangdong to direct flood control efforts, the report said.
The rainstorms have battered five cities in the province including the provincial capital Guangzhou, triggering heavy flooding in some areas and affecting about 650,000 people, Xinhua reported. Water levels of some of the rivers have crossed warning lines.
The report said more than 2,600 homes have been destroyed. Highest precipitation of nearly 340 millimeters (13 inches) was reported in Qujiang district as of 11 a.m. Thursday.
The rainstorms were forecast to continue Friday.