53 people were killed and several went missing in the rains, state-run television CCTV said.
Earlier, official Xinhua news agency reported that rainstorms have triggered flooding and landslides in some places.
Officials have been sent to undertake disaster relief operations in worst-hit Guangdong and Jiangxi Province.
In Guangdong, rainstorms battered 173 townships in five cities, including the provincial capital Guangzhou, triggering heavy flooding in some areas.
The water levels of some rivers in Guangdong have surpassed warning lines, and an offshoot of the Beijiang River saw the worst flooding in a century, according to the headquarters.