Analysis from the perspective of structural dynamics was done to find out how the structure of regenerator affects the thermoacoustic engine. Based on ordinary stack, models of pin array and stacks with fins or with micro-slots were created in ANSYS. Structural dynamics analysis was carried out on thermoacoustic engine with all the three stacks. The results showed that the resonance frequency of engine with ordinary stack occurred at 150Hz, which changed with the special-shaped regenerators, and the maximum strain amplitude appeared at a higher order modality. And it has indicated that the optimization of the regenerator's structure is an effective way to improve the performance of thermoacoustic engine.