Vertical axial flow pump device has the characteristics of large flow and low head, which is widely used in pumping station projects with head of 3–9 m. In order to study the influence of the timing effect of the impeller relative flow channel and guide vane on the flow field and pulsation in the axial flow pump device, the whole flow channel of the vertical axial flow pump device was taken as the research object. The reliability of the numerical simulation was verified by physical model test. The flow field characteristics and pressure pulsation characteristics of the inlet and outlet regions of the impeller, the guide vane and the campaniform inlet conduit at different timing positions of the impeller under different flow rates were analyzed. The results show that the pressure coefficient distribution of the impeller inlet of the vertical axial flow pump device presents four high-pressure areas and four low-pressure areas with the rotation of the impeller. The pressure pulsation at the inlet and outlet of the impeller is mainly affected by the rotation of the impeller, and the main frequency is 4 times the rotation frequency amplitude of pressure pulsation decreases with the increase of flow rate. When the flow rate increased from 0.8 Qbep to 1.2 Qbep, the average velocity circulation at the guide vane outlet decreased by 12%; there is an obvious negative value region of the internal regularized helicity of the guide vane. When the flow rate increases from 0.8 Qbep to 1.2 Qbep, the amplitude of the pressure pulsation coefficient at the outlet of the guide vane decreases gradually, with a decrease of 94%. When the flow rate is 1.2 Qbep, the main frequency and the secondary frequency of the pressure pulsation are both low-frequency, with obvious low-frequency pulsation characteristics. Under the small flow condition of 0.8 Qbep, the outlet flow fluctuation of seven guide vane was 18.9% on average, and the flow variation of each guide vane was large. Under the optimal flow condition of 1.0 Qbep and large flow condition of 1.2 Qbep, the outlet flow fluctuation of 7 guide vane is 4.7% and 0.56% on average, and the flow change of each guide vane is stable. The outlet flow of the guide vane is mainly concentrated in two guide vane slots of the guide vane, and the flow ratios are 30.56%, 30.14% and 29.16% under three flow conditions, respectively. The research results provide a scientific basis for the optimization design and stable operation of vertical axial flow pump device.