It is important to study the vibration characteristics of the impeller rotor of an axial flow pump for avoiding resonance and ensuring the safe and stable operation of the pump. Based on the fluid-structure coupling method and considering the compressibility of fluid, the coupling equation of fluid and solid is solved by inserting APDL command flow into ANSYS Workbench platform. The natural frequencies of the runner of horizontal axial flow pump in water and the reduction coefficients of each order of frequencies are obtained, and the distribution of each order of modes is analyzed. Additional mass theory is used to analyze the reasons for the reduction of natural frequencies. The results show that the natural frequency of the impeller of an axial flow pump decreases due to the water medium. The increase of the vibration quality of the whole system caused by the water body vibration is the fundamental reason for the reduction of the natural frequency of the impeller. The damp dissipation of the water body will lead to the decrease of the amplitude of the impeller in water.