The occurrence and development of centrifugal pump rotating stall is closely related to disturbance in the incoming flow. The seal clearance leakage is an inherent disturbance in the impeller incoming flow of centrifugal pumps. In order to investigate the seal clearance leakage influence on the rotating stall characteristics, the flow field numerical simulation of a centrifugal pump under rotating stall flow conditions with and without seal clearance are carried out. It is found that under the 0.4Q0 rotating stall condition with seal clearance leakage, the “λ” special shaped high-velocity region distribution along the blade leading edges are strengthened, which lead to larger scale of stall vortices. And the periodicity of the separation vortex evolution is more obvious under the condition with leakage. For a specific stall vortex development process, at the initial format stage, there is a notable disturbance characteristic of medium frequencies band that of 2–3 times the rotation frequency in the pressure fluctuation near the blade leading edges, which is significantly different from that under the condition without leakage. The vorticity analysis shows that this disturbance is closely related to the leakage induced vortices. Affected by the seal clearance leakage disturbance, the stall rotating propagation frequency is reduced from 0.143 times the impeller rotational frequency to 0.103 times. Meanwhile, the fluctuation intensity in the impeller channels is greatly enhanced. Therefore, by judging the special fluctuation frequencies, regularity, and intensity trend in the monitoring signal, it can not only be used to guide the safe operation of centrifugal pumps under off-design conditions but also serve as the basis for judging the wear of the seal, which has important practical significance.