The pumping station is a water conservancy facility which integrates electrical equipment, hydraulic machinery and hydraulic structures. Its biggest characteristic is that the load is dynamic load with large frequency and strong concealment. Therefore, it is very important to confirm the vibration source and cause in the safety appraisal of pumping station. In order to solve the problem of vortex belt, vortex and hydraulic pulsation in the water delivery pipeline of an irrigation pump station when multiple units are running, the pump house has a large vibration. Through the establishment of a three-dimensional finite element model of the structure of the pumping station building, using ABAQUS software and Lanczos method to extract the structural mode of the pumping station building, the natural vibration frequency and vibration mode of the pumping station building are analyzed In this paper, the vibration source and the cause of the vibration of the power house are determined, and the possible vibration source and frequency characteristics of the pumping station are determined. The vibration source is verified and analyzed with the theoretical calculation value of the main excitation source frequency of the pumping station unit. The results show that there is resonance phenomenon between the excitation source frequency of the pumping station unit and the natural vibration frequency of the powerhouse structure. The research results can provide a theoretical basis for the maintenance and reinforcement of the pumping station.