To investigate the dynamic characteristics of micro-structure in a Micro-electro-mechanical System(MEMS) at a low temperature environment, a theoretical model was established and the effect of environmental temperatures on the resonant frequency of a micro-cantilever was researched. Then,a dynamic testing system for MEMS at low temperature was developed. In testing,a thermoelectric cooling refrigerator was utilized to generate the low temperature environment and the piezoelectric ceramic was used as the driving source to establish the base excitation device. Through the base impact excitation, the resonance frequencies were obtained by analyzing the impulse response signals and the frequency response of micro-cantilever was tested by using a laser Doppler vibrometer. The dynamic testing experiments for the silicon micro-cantilever were carried out from -50 ℃ to room temperature. Obtained results show that the resonance frequency slightly increases with the decreasing temperature, and it is consistent with that of the theoretical analysis. The temperature dependency of frequency is about -0.263 Hz/K,which is a little smaller than that of the theoretical results. The measurement device is very effective to carry out dynamic testing of microstructures from -50 ℃ to room temperature.