A stroboscopic microscopic interferometry based on Fourier transform method(FTM) is put forward to measure the out-of-plane motion of micro-resonator and micro-cantilever.The periodic motion of microstructure is excited.The cycle of a periodic motion is divided into some motion phases.The interferogram sequence with different motion phases is collected via stroboscopic photography.FTM is applied to calculate the wrapped phase distribution of each interferogram,and the out-of-plane motion characteristics are extracted from phase unwrapping curves of wrapped phase distribtions with different motion phase.Compared with temporal phase shifting interferometry,only one interferogram per motion phase is needed,and a lower acquisition time is obtained.Experiment study shows the measurement accuracy of out-of-plane motion is better than 20 nm.