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Stroboscopic interferometer system is a kind of excellent measurement system for MEMS characterization which can measure the motion of whole MEMS structure in the vision filed, and the dynamic properties such as eigenfrequency and vibration modal shape can be obtained. This paper presents a data analysis method for MEMS dynamic characterization based on stroboscopic interferometer system, which establishes an element dynamic model by discretizing the MEMS structure into finite elements. On the basis of analyzing the amplitude and phase difference of these elements, dynamic equation of the element is established. As an example, a dynamic model of micro cantilever was established and the measurement data of an AFM cantilever were analyzed by this method. The dynamic properties such as thickness distribution and the damping distribution were extracted.