The influence of O-ring deformation and piston radius on the output performance of the PZT hydraulic pump was analyzed. The O-ring deformation was examined by using the finite element method. Besides, an experiment was set up to validate the flow rate result. The obtained results reflect that the gap height between check valve and a solid surface has a major impact on check valve’s natural frequency in liquid. The flow rate value and optimal frequency of the PZT pump can be improved by the design of the check valve.