A method of removing a photoresist layer is provided. An ion implantation process has been performed on the photoresist layer to transform a surface of the photoresist layer to a crust and a soft photoresist layer remains within the crust. The method includes performing a first removing step to remove the crust, such that the soft photoresist layer is exposed. Thereafter, a second removing step is performed to remove the soft photoresist layer. The first and the second removing steps are performed in difference chambers, and a temperature for performing the first removing step is lower than that for performing the second removing step and lower than a gasification temperature of a solvent in the soft photoresist layer.