In this article, a practical iterative algorithm for tuning the parameters of notch filter is presented to suppress highfrequency resonance in ultra-precision motion control. Notch filter is a useful tool to suppress middle-and highfrequency resonance to improve control precision. The traditional tuning method for it depends on the Fourier transform of the positioning error or the modal analysis of the motion stage, which cannot get the optimal control performance. The proposed algorithm can be used to tune the parameters of notch filter iteratively through minimizing a cost function of the positioning error, and it needs only measurement signals in actual motion system rather than detailed model of the motion stage. The proposed algorithm can suppress mechanical resonance and meanwhile minimize positioning error, which are demonstrated by experimental results in wafer stage of photolithography.