An official in Liuhuang township in Meizhou told Reuters that thousands of residents were in temporary shelters after their homes were flooded by the Hanjiang river where water was 4.44m above the danger level on Monday.
"Rice crops were just devastated. It's not far from harvest but they have all been destroyed,"the official said by telephone.
He said the rain had stopped by early Tuesday and water had begun to recede, but power was only partially restored.
Parts of China are regularly hit by heavy rains and flooding every summer, although officials say the storm season is only just getting under way in the south.
Experts last month warned that the Yangtze could flood badly this year for the first time since 1998 when flooding killed more than 3,000 people.
Meanwhile some northern regions are being hit by heatwaves, with temperatures in parts likely to reach 40 degrees Celsius, the meteorological administration said.