Some resonant peaks in the frequency response curve of a hydrophone usually appear at the resonant frequencies of the sound-transparent cap, which make the frequency response curve distorted and the working band narrowed. Thereby, it is necessary to forecast the resonant frequencies of the sound-transparent cap accurately. According to the working environment of a MEMS Hydrophone, this paper analyzes the resonant frequencies of the sound-transparent cap based on the Fluid-Structure Interaction(FSI). Firstly, the effect of fluid action on the FSI of the sound-transparent cap was analyzed in theory, and it shows that the resonant frequencies of the sound-transparent cap will be lowered by the fluid action.Then, the vacuum mode and coupling mode of the chip and sound-transparent cap were simulated by LMS V irtual.lab, respectively. Finally, the MEMS vector hydrophones with and without sound-transparent cap packaging were tested in a shaking table and a standing wave tube to verify the above analysis. The results indicate that the actual first-order resonant frequency of sound-transparent cap in water is 550 Hz, which is the same as the simulation and makes the working frequency band of hydrophone narrowed. The results show that the research on coupling modal analysis of sound-transparent cap and predicting the properties of the hydrophone accurately would provide the guarantee for further optimization and improvement of the hydrophones.