To improve shutdown safety for agricultural irrigation pumping stations, this study investigates the synchronous and asynchronous shutdown processes of a pump device using numerical simulations validated by model tests. The results show that during the synchronous shutdown process, vortices appear on the inside of gate as its opening decreases, and their ranges expand accordingly. When the gate is 90% closed, negative pressure zones emerge in the outlet passage. As the gate continues to close, the strength and range of negative pressure zones keep expanding, and air is drawn into the outlet passage. After the gate is fully closed, the water flow starts reciprocating motion with strength attenuation due to inertia and water pressure. Compared with the synchronous shutdown method, the asynchronous shutdown-F1 to F4 achieved significant reductions results: the maximum reverse rotation rate decreased by 17.74%, 39.59%, 59.18%, and 83.35%, respectively, while the maximum reverse volumetric flow rate decreased by 17.32%, 38.45%, 59.20%, and 79.19%, respectively. Furthermore, in asynchronous shutdown-F4, no negative pressure occurs in the outlet passage, even if the gate closes suddenly. Therefore, the asynchronous shutdown method is a safer alternative for irrigation pumping stations. This study proposes more appropriate shutdown methods for pumping stations, which has significant practical value.