In order to reduce the surface roughness of workpiece during milling process, a method of generating secondary milling trajectories based on residual wave peaks was proposed. According to the position of the residual wave peaks in one milling process, the corresponding wave crest elimination trajectory was generated to eliminate the residual wave crest in one milling process, thereby reducing the roughness of the milled surface and improving the surface quality. A secondary milling trajectory generation method based on residual wave peaks was given based on the STL model, and a milling experiment was performed using this method. The experimental results show that the surface roughness of the experimental parts after secondary milling is significantly reduced, and the wave height is significantly reduced, which verifies the feasibility of this method.