The budget carrier plane left Hangzhou, capital of Zhejiang province, after 7 a.m. and was headed for Xishuangbanna Dai in Yunnan province when the rat was discovered, Xinhua news agency reported.
The airliner confirmed it was not a domesticated pet and they were looking into how it got on the plane.
Rats are infamous for chewing up electric wire, a huge safety issue on an airplane as they could sabotage the flight control system.
They could have gotten into the plane by following catering vans and other cargoes, Xinhua quoted sources as saying.
Airline employees fumigated and disinfected the plane.