At least 24 people died and more than 100 were injured after heavy rain moved through five provinces and a "super-tornado" carrying huge hailstones hit one city.
The China Meteorological Centre says the severe weather is expected to continue until Sunday.
"All parts of southern China should take measures to be on guard against the negative influence of thunder and lightning, high wind and hail," the centre said.
The storms reached their peak on Wednesday when local media reported a capsized ferry in the city of Nanping in the south-eastern province of Fujian, causing the deaths of 11 people with four still missing.
Gale winds of up to 75 kilometres reportedly blew down 2,000 structures, damaging a further 248,000.
Nine people were killed in Dongguan, in Guangdong province in the south.
Online reports showed images from the city of a car windscreen which appeared to have been smashed by egg-sized hailstones.
Many of the dead in Dongguan were trapped in collapsed buildings.
Another 148 people were injured, including 11 who were critically ill, the report said.
State-run news agency Xinhua put the death toll at 24.
Other provinces affected by storms and torrential rain on Wednesday were nearby Jiangxi, Hunan in central China and Guizhou in the south-west.
A total of 1.53 million residents have been affected by severe weather and 215,000 people were forced to relocate, Xinhua said, citing the Ministry of Civil Affairs.