During the spacecraft′s in-orbit running, its structure could get a micro angular vibration due to various moving parts inside, which has relatively small amplitude and high frequency and could result in quality reduction of the optical load′s imaging. With broad bandwidth and high sensitivity, the FOG can output angular increment in a sample cycle, making it the perfect sensor of micro angular vibration. But FOG can′t be sampled evenly considering the spacecraft′s whole scheduling. This paper proposes a frequency spectrum analysis method for nonuniform sampling, which transforms time sequence in a complete nonuniform sampling cycle to the fourier space to obtain original signal′s amplitude and frequency so as to achieve high precision measurement of the micro angular vibration. The method has a precision better than 0.04″, which was validated by digital simulation and 6-DOF micro vibration test.