Though they were rescued, the boy later succumbed to his injuries.
Earlier, authorities moved about a million people to safe places in the two coastal provinces ahead of the impending arrival of the Morakot, the eighth such tropical storm to hit China this year.
Over 490,000 residents of Zhejiang and more than 505,000 from Fujian have been evacuated to safer areas, authorities said.
Morakot, listed as a category 1 storm on a 1-4 scale by the Tropical Storm Risk forecasting service, had killed one person and left 10 injured and four people were missing in Taiwan before heading towards China.