The Shenzhen meteorological station forecast downpours of up to 200 mm would hit the city Wednesday and Thursday.
Middle and primary schools in Shenzhen have suspended classes.
As of 8 a.m., no casualties had been reported, the city's flood control authorities said.
By 11 a.m., Shenzhen airport had cancelled two domestic fights:
One inbound and one outbound, while 10 outbound flights had been delayed and seven scheduled to depart between 11 a.m. and 1 p.m. were also delayed.
A flood prevention emergency response plan was activated on Wednesday in eastern Jiangxi Province. Heavy rains of 80 mm to 200 mm were forecast in the province's eastern and southern areas from Wednesday through to Saturday.
The storm was forecast to hit Ganzhou City, in Jiangxi, late on Wednesday and was expected to affect the province for 36 hours, the provincial meteorological station said.
Two teams from Jiangxi flood control headquarters had been dispatched to the affected areas to help with evacuations and preparations against floods, landslides and mud-rock flows.