The dynamic testing system for MEMS in low temperature environment has been developed. A thermoelectric cooling refrigerator was utilized to generate the low temperature environment. The base excitation device was established using the piezoelectric ceramic as the driving source. A vacuum chamber was designed to protect the micro-structure from the humid air. Through the base impact excitation, the resonance frequencies are obtained by analyzing the impulse response signals. The frequency response of micro-cantilever was obtained by using both BIST method and laser Doppler vibrometer. The dynamic testing experiments for the silicon micro-cantilever were carried out from -50°C to room temperature. The result shows that the resonance frequency slightly increases with the decreasing temperature. The measurement device is effective to carry out dynamic testing of microstructure from -50°C to room temperature.