Forecasters on Friday were predicting more rain for the area where the rising waters have already forced the evacuation of 1.4 million residents, officials said.
Water reached the top of telephone poles in parts of the heavily populated south, where people used small boats to navigate flooded streets.
Government forecasters warned of more torrential rains in the densely populated south, especially around the Pearl River Delta northwest of Hong Kong - the heart of China's booming export industries.
Damage was worst in southern China, where rains and mudslides have killed at least 97 people this week and left another 41 missing, the report said. It said people were evacuated from flood-prone areas across a swath of five southern provinces.
Nationwide, a total of 137 people are missing, the Xinhua news agency reported. So far, most damage in Guangdong appeared to be to farms, with export-oriented factories largely unaffected, said Ruby Zhu, China economist for the Hong Kong General Chamber of Commerce.
"It doesn't seem serious now," she said. "But if it gets more serious, we're not sure what will happen in Guangdong province."
The death toll was higher than most of the rainy seasons of the past decade, though still below that of 1998, when 4150 people were killed in summer flooding in central and northeastern China, Xinhua said.
In Guangdong, roads and rail lines were cut by floodwaters, including the main Beijing-Hong Kong railway, Xinhua said.
Residents navigate a street in
the southern city of Wuzhou
In the provincial capital, newspaper photographs showed floodwaters so high in one town that they nearly reached the top of telephone poles.
High water levels could spread sewage, polluting drinking water and raising health risks, as well as damaging crops, said Alistair Henley, the Beijing representative of the International Federation of Red Cross and Red Crescent Societies.
"There will be a lot of suffering particularly for the rural people in neighbouring counties," Henley said.
Flooding in parts of Guangxi, west of Guangdong on China's southern coast, was the worst in a century in the poor, mountainous region, state media said.
About 760,000 people were evacuated from areas in Guangxi, state television said. Some were being housed in tents and hastily erected shacks, said Tao Yaoming, a rescue official in the riverside town of Luzhai in Guangxi.
People take to the balconies to
avoid the waters in Wuzhou
"All those impacted by the floods are being handled properly," Tao said. Authorities in Macau, the former Portuguese colony west of Hong Kong at the mouth of the Pearl River, issued a flood warning, saying the rain-swollen river could rise to as much as 1m (3ft) above normal, Xinhua said.
China suffers hundreds of flooding deaths every summer in its south and northeast. The impact of seasonal rains is magnified by environmental damage from decades of intensive farming and tree-cutting that have left denuded hillsides unable to trap rain.
Millions of people live in vulnerable areas on reclaimed former flood plains.
Newspapers showed soldiers and police rowing boatloads of residents down flooded streets. News reports said floodwaters in some parts of Guangxi reached the third floor of buildings.
In Guangxi, about 42,000 people were evacuated from low-lying areas of the industrial city of Wuzhou in case a surging river that flows through the city overwhelmed protective dikes, the government said. High school entrance exams in Wuzhou were suspended.