The RNG k-ε model turbulence model is used to carry out a CFD numerical simulation of the dual-flow channel pumping station. Through the model test, the accuracy of the numerical simulation of the dual-flow channel pump device is verified. Using the harmonic response analysis method, the water pressure fluctuating load calculated under different startup conditions under the design water level is applied to the pumping station. In this way, the dynamic response law of the pump station structure under the action of water pressure pulsation is studied. The calculation results show that the values of pressure pulsation in the drainage condition and the water diversion condition are relatively close, and the main difference is the difference in the water levels of the inlet and outlet water. Under different working conditions, the amplitude of the pumping station building basically shows the characteristics that the vertical amplitude is greater than the horizontal amplitude. The maximum dynamic displacement under drainage condition is greater than that under the diversion condition, and the maximum dynamic displacement appears at the control gate. Under the three working conditions, the maximum dynamic stress of each characteristic part of the pumping station building is low. The maximum total dynamic stress under the drainage condition is greater than that under the diversion condition.