Abstract: In order to clarify the interference between the multistage impeller and the side channel and the flow form between the pump stages, so as to improve the hydraulic performance and operation reliability of the side channel pump, a multistage side channel pump with front centrifugal impeller and two-stage radial impeller was selected as the research object. The ANSYS CFX was used for the simulation in this work, and then the influence of different clocking position on pressure pulsation inside the impeller and at the outlet was investigated by Fourier variation and wavelet decomposition methods. The results show that the appropriate clocking position can effectively improve the pressure pulsation amplitude of multistage side channel pump. The optimal clocking position angle of the side channel pump is inversely proportional to the impeller stage and proportional to the blade angle. After the optimal adjustment of the clocking position, the overall vibration and the pressure pulsation at the outlet part can be reduced. The research result provides an effective reference for the design of the multistage side channel pump.