The boy later died, according to the city's flood-control headquarters.
In Zhejiang, more than 3.4 million people suffered property losses as hundreds of villages were flooded and more than 1,800 houses collapsed.
The National Meteorological Centre said violent rainstorms would continue in south Jiangsu, southeast Anhui, northeast Jiangxi, Shanghai, most parts of Zhejiang and Fujian, and Taiwan over Monday.
The centre also warned of possible flooding near Taihu Lake, Jiangsu Province, as downpours reached 100 to 130 mm.
Meanwhile, Morakot also caused losses in Taiwan.
According to the island's disaster response centre, Morakot killed 12 people and injured 52, while 32 were still missing as of Monday.
Taiwan's meteorological department lifted the typhoon alert at 10 a.m., but continued to forecast rainstorms in the area south of Miaoli County.