The motion characteristics of microstructure are corresponding to the performance and reliability of MEMS devices. To realize the measurement of rotation motion to get the characteristic of MEMS resonators in every moment, a method is presented for measuring the MEMS rotation angle based on the combination of Fourier-Mellin transform and phase correlation. By using the rotational invariance of Fourier-Mellin transform, the motion in space coordinate is transferred to parameters of Log-Polar coordinate, and the rotation motion is projected to displacements. Then the displacements are measured by a phase correlation method to realize a sub-pixel motion measurement. Experimental results show that the proposed algorithm can reach angle measurement resolution of 0.01° with less calculations and anti-interference ability.