Morakot made landfall on Xiapu, a county in eastern China's Fujian province, carrying heavy rain and winds of up to 74 miles per hour, according to an official at the China Meteorological Administration who refused to give his name or provide other details.
Taiwan, meanwhile, was recovering after the storm dumped more than 80 inches 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 Center said a woman was killed when her vehicle plunged into a ditch in Kaohsiung county in heavy rain Friday, and two men drowned in Pingtung and Tainan respectively. It said that 31 were missing and feared dead.
About 1 million people were evacuated from China's eastern coastal provinces by early Sunday - more than 490,000 people in Zhejiang and 480,000 others in neighboring Fujian. Authorities in Fujian called 48,000 boats back to harbor.
Thirty-nine outbound flights from Wenzhou city in Zhejiang were canceled Sunday, the official Xinhua News Agency said.
Morakot hit Taiwan late Friday but traversed the island Saturday.
Taiwan's Disaster Relief Center reported Sunday that flash flooding had washed away a makeshift home in southern Kaohsiung, leaving 16 people missing. Three were swept away in southeastern Taitung county, including two policemen helping to evacuate villagers.
Twelve others were missing, including three fishermen from a capsized boat and three others whose cars fell into a rain-swollen river, it said.
In southern Pingtung county, 4,000 people were stranded in inundated villages waiting for police boats to rescue them, news media reported.
In Taitung county, a six-story hotel collapsed and plunged into a river after floodwaters eroded its base, but all 300 people in the hotel were evacuated and uninjured, officials said.
Morakot is the first typhoon to hit Taiwan this year. Typhoons frequently move in between July and September, often causing injuries and deaths in mountainous regions prone to landslides and flash floods.
In the northern Philippines, the typhoon and lingering monsoon rains left 21 people dead and seven others missing in landslides and floodwaters, including three European tourists who were swept away Thursday, the National Disaster Coordinating Council said Sunday.
The bodies of a Belgian and two French citizens were found Friday, the council said.
More than 83,000 people in 93 northern villages were affected by floods and landslides, including 22,200 who fled their homes, it said. Displaced people began returning home as the weather cleared, it said.
Meanwhile, officials said rescue helicopters and ships were still searching for about 10 Chinese crew whose ships were caught in Tropical Storm Goni, which made landfall in Guangdong on Wednesday, swept the coastal areas of Hainan Thursday and Friday but weakened into a tropical depression by Sunday.
By Associated Press Writer Gillian Wong; AP writers Annie Huang in Taipei and Jim Gomez in Manila contributed to this report