Stall usually occurs in the hump area of the head curve, which will block the channel and aggravate the pump vibration. For centrifugal pumps with guide vanes usually have a clocking effect, the stall characteristic at different clocking positions should be focused. In this paper, the flow field of the centrifugal pump under stall conditions is numerically simulated, and the rotor–stator interaction effects of the centrifugal pump under stall conditions are studied. The double-hump characteristic is found in the head curve by using SAS (Scale Adaptive Simulation) model. The hump area close to the optimal working condition is caused by hydraulic loss, while the hump area far away from the optimal working condition point is caused by the combined action of Euler’s head and hydraulic loss. The SAS model can accurately calculate the wall friction loss, thus predicting the double-hump phenomenon. The pressure fluctuation and head characteristics at different clocking positions under stall conditions are obtained. It is found that when the guide vanes outlet in line with the volute tongue, the corresponding head is the highest, and the pressure fluctuation is the lowest. The mechanism of the clocking effect in the centrifugal pump with guide vanes is obtained by simplifying the hydrofoil. It is found that when the downstream hydrofoil leading edge is always interfered with by the upstream hydrofoil wake, the wake with low energy mixes the boundary layer with low energy, which causes small-pressure pulsation. The results could be used for the operation of centrifugal pumps with guide vanes.