In order to analyze the vibration characteristics and causes of structural vibration of the Third Huaian Pumping Station, a three-dimensional finite element model was established, using the finite element-based dynamic analysis method, according to the structural characteristics of the bulb tubular pumping station. The finite element model was used to analyze the self-vibration characteristics, dynamic responses, and causes of vibration; measures for vibration resistance and reduction were also studied. The results show that the main cause of vibration of the Third Huaian Pumping Station is the resonance vibration induced by the substructure and fluctuating pressures of water flow. Under fluctuating pressures of water flow, the structures of the Third Huaian Pumping Station show large dynamic displacements, approaching the maximum allowable displacement of architectural structures. Corresponding measures for resisting and reducing vibration were developed by increasing the floor thickness and beam section size of the pumping station.