Floods in Hunan, Guangdong, Guangxi and Guizhou left one dead and five missing.
More than 11,000 people were relocated and 4,900 people received emergency aid, such as food and drinking water, the Ministry of Civil Affairs said.
Torrential rain has left five people missing in southwest China's Guizhou Province.
Storms had forced nearly 4,000 residents to temporarily relocate.
The rain damaged more than 520 hectares of crops and over 360 houses collapsed, state-run Xinhua news agency reported.
More storms are expected in next four days.
In east China's Jiangxi Province, more than 260 teachers and students were trapped in a primary school by flooding today and were relocated to safer places.
Hail in north China also disrupted the Dragon Boat Festival holiday, causing the death of one person.
Hail stones accumulated on the road to a depth of more than 10 cm in some places, provincial meteorological station said.
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