The disaster threatens to cause price hikes and the availability of China's famous dish, Peking Duck, as the farm is a main supplier to Beijing's restaurant chain, Quanjude, famous for its trademark Quanjude Peking Roast Duck.
The birds died on Friday when extremely high winds swept through hundreds of duck pens, inflicting losses of around 3 million yuan ($440,000).
"Luckily 12,000 breeding ducks were in another place and survived, so there is hope that we will restore the farm in a month," the Danwei newspaper quoted a manager as saying.
At least 18 people died in China last week in flash floods and landslides.
Weather forecasters expect more heavy rain to hit the south of the country over the next three days.