The invention provides a method for performing rapid thermal annealing process by using thermal annealing equipment. The method comprises the following steps: separately setting the thermal annealing equipment according to first and second parameters in an idle state and a working state, setting at least one previous heating cavity in a plurality of heating cavities of the thermal annealing equipment as a distinctively set heating cavity, wherein the set temperature of the distinctively set heating cavity in the first parameters is lower than the set temperature of the distinctively set heating cavity in the second parameters, so that when the thermal annealing equipment converts from the idle state into the working state, the temperature difference between a substrate primarily put in the thermal annealing equipment and the substrate put in the thermal annealing equipment in the stable working state in the working state is reduced, thereby reducing the occurrence of TTP mutation, reducing the risk of discarded products, improving the yield of products and increasing the economic values of the products.