Media reports showed submerged cars, marooned shops and apartments as well as landslides and mudslides.
Fuzhou received up to 554mm of cumulative rain on Tuesday, the national forecaster said, for an hourly record of close to 150mm.
That surpassed the volume brought by Typhoon Doksuri in late July, which ripped through Fujian to cause floods and losses of US$2 billion, state media said.
Fuzhou closed subway lines and suspended train services, while schools shut for a second day.
The floods have hit many cities in Fujian, exposing the fragility of urban drainage and other infrastructure, state-backed The Paper quoted a provincial official, Chen Yunong, as saying.
Waterlogging in both old cities and new urban areas needs to be tackled, Chen said.
Putian and Quanzhou were among six cities elsewhere in Fujian flagged as being at risk of flash floods and landslides. The provincial government told local authorities to prepare to move out people from areas likely to be the hardest hit.
The rains are expected to last until Friday in central and southern parts of the province, where Typhoon Haikui hit land early on Tuesday, before losing strength and being downgraded to a tropical storm.