Another 300 houses collapsed and thousands of acres of farmland were inundated, Xinhua said.
Transport links cut
Many transport links were cut with major roads and several airports closed and flights cancelled.
Residents in Shanghai were told to brace for heavy rain as the storm approached China's financial capital, bringing up to 90mm of rain an hour.
Morakot, which means "emerald" in Thai, struck the Chinese mainland after triggering the worst flooding in Taiwan 50 years, leaving dozens of people missing and toppling a six-storey hotel.
It earlier lashed the Philippines, killing at least 21 people.
The typhoon made landfall in Fujian province on Sunday, carrying heavy rain and winds of 119kph, according to the China Meteorological Administration.
In Fujian, about 48,000 boats were called back to harbour and bus services in the provincial capital, Fuzhou, were suspended.
|The storm has already flooded thousands of acres of farmland [Reuters]
The storm had been expected to veer up to the north and bring strong winds and heavy rains to Shanghai, the meteorological administration said, but the commercial capital appeared to escape the brunt of the typhoon, which was later downgraded to a tropical storm.
Taiwan, meanwhile, is cleaning up after the storm dumped more than 200cm of rain on some southern counties on Friday and Saturday, the worst flooding to hit the area in half-a-century, the Central Weather Bureau reported.
Taiwan's Disaster Relief Centre said a woman was killed when her vehicle plunged into a ditch in Kaohsiung county in heavy rain on Friday, and two men drowned in Pingtung and Tainan.
Thirty-one other people were missing and feared dead.