With the development of MEMS, the mechanical properties of micro crystals must to be determined to know the defect, reliability and characterization of MEMS. Young’s modulus is one of the most important properties, which indicates the ability of resisting the elastic deformation. Many methods, such as natural frequency measurement, beam bending tests, membrane bulge test and uniaxial tension test, have been used to measure Young’s modulus of Si, SiN and metals. But there are some limitations when they are used to measure micro crystals in MEMS. This paper puts forward a high accuracy and convenient method----using Raman spectrum to measure Young’s modulus of micro crystals in MEMS, and sets up the measurement system. Measured Young’s modulus of Si and GaAs in  crystallographic orientation are 161.113GPa and 84.128GPa respectively, which correspond with the Yong’s modulus in common use now. Based on the values, it can be analyzed if there are some defects in the micro crystals.