The present invention provides a method of manufacturing a semiconductor device. The method at least comprises the following steps. First, the semiconductor device, which comprises a gate, a gate dielectric layer, an active layer, a source and a drain, is manufactured. However, the semiconductor device has a plurality of defects, and the active layer is a metal oxide thin film. After annealing the semiconductor device, it will be transferred into a chamber. A final step of injecting a supercritical fluid carried with a co-solvent into the chamber is then performed to modify the abovementioned defects.