Based on the example of one underground powerhouse, the paper established the three-dimensional finite element model of the powerhouse by using finite element analysis software ANSYS, deeply researched the influence of different boundary conditions on vibration characteristics of structure. The free vibration signal of the floor construction can be extracted from its vibration frequency with the Random Decrement Technique according to the signal of starting and ending the machine. At the same time, according to the harmonic response calculation results ,the resonance frequency of floor structure can be estimated by analyzing the vibration characteristics of beam structure in the function of hydraulic pulsation.