This paper employs the integral-averaged method of thickness to approximate the periodical flows in a piezoelectric micropump, with a shallow water equation including nonlinearity and viscous damp presented to characterize the flows in micropump. The finite element method is used to obtain a matrix equation of fluid pressure. The fluid pressure equation is combined with the vibration equation of a silicon diaphragm to construct a liquid-solid coupled equation for reflecting the interaction between solid diaphragm and fluid motion in a micropump. Numerical results of a mode analysis of the coupled system indicate that the natural frequencies of the coupled system are much lower than those of the non-coupled system. The influence of additional mass and viscous damp of fluid on the natural frequencies of the coupled system is more significant as the pump thickness is small. It is found that the vibration shape functions of silicon diaphragm of the coupled system are almost the same as those of the non-coupled system. This paper also gives the first-order amplitude-frequency relationship of the silicon diaphragm, which is necessary for the flow-rate-frequency analysis of a micropump.