The low frequency pressure fluctuations in axial flow pump with variable inlet guide vane were studied. The numerical method based on the RANS equations and SST k-ω turbulence model was used to simulate unsteady flow in the axial flow pump. The hexahedral meshing scheme was used for the whole computational domain, particularly with O-grid around the blades. The multiple reference frame approach was applied to solve the rotor-stator interaction problem in steady simulation and it was changed to the sliding mesh technology in unsteady simulation. The mass flow rate was adopted at the inlet section and static pressure at the outlet section. No-slip conditions were applied to the whole wall boundary. The effects of variable inlet guide vane on pump performance were firstly investigated. Then through analyzing the spectra of pressure fluctuation at different pressure survey points, the variation of low frequency pressure fluctuation by adjusting the angles of inlet guide vane was presented. The flow field in outlet guide vane under small flow condition was also presented. The results showed that the predicted results were in good agreement with the experimental data. When the angle of inlet guide vane was negative, the pump head was increased due to the prewhirl regulation, and the efficiency was basically kept unchanged at small flow rate and it was slightly increased at large flow rate. When the angle of inlet guide vane was positive, both the pump head and the efficiency were decreased, and the efficiency dropt greatly at large flow rate because of the large hydraulic loss caused by inlet guide vane. At small flow rate, the vortex in the exit guide vane can cause low frequency pressure fluctuation, which was consistent with the vortex frequency. When the axial flow pump was operated under off-design condition, the variable inlet guide vane could decrease the angle of attack at the impeller entrance and further descend the amplitude of low frequency pressure fluctuation.