The thesis details the influence of harmonic waves in the short circuit current to the rate of rise protection. On the base of it, an algorithm is presented to handle the sample date for eliminating the influence of harmonic waves, at the same time considering the characteristics that DC component in transient short circuit current of subway can be shown with exponential form and the principle that the integral result of AC component for a cycle is zero. By simulation with Labwindows/CVI, it is proved that the algorithm can smooth the transient electric current wave and the error is very small.