For the unsteady flow in hump region of waterjet propulsor under low flow conditions, computational fluid dynamics method was used to study the instability characteristics. The results show that the head and efficiency of propulsion pump significantly decrease with the decrease of the flow rate, the head curve shows a hump characteristic of positive slope between 0.42Q_d and 0.8Q_d, while the internal flow field becomes turbulent, accompanied by flow separation and backflow. The magazine slotting technique was used to controll the unsteady flow, and the hump phenomenon was significantly improved. The head and efficiency at the deep stall operating point were increased by about 147.6% and 70.3% respectively compared to those of the original model under the optimal slot structure parameters. On one hand, the magazine slotting can rectify the inlet flow and play a role in reducing the pre-swirl and increasing the axial inlet velocity. On the other hand, it can inhibit the formation of vortex in mainstream area and low-frequency pressure flluctuations at impeller inlet.