The pumps in multistage drainage pumping stations are often subject to frequent start-up and shutoffs during operation because of unreasonable start-up depths of the pumps; this will reduce the service lives of the pumps. To solve this problem, an optimization method for minimizing pump start-up and shutoff times is proposed. In this method, the operation of pumps in pumping station was optimized by constructing a mathematical optimization model. The storm water management model (SWMM) and particle swarm optimization (PSO) method were used to solve the problem and the optimal start-up depth of each pump is obtained. Nine pumping stations in Beijing were selected as a case study and this method was applied for multistage pumping station optimization and single pumping station optimization in the case study. Results from the case study demonstrate that the multistage pumping station optimization acquired a small number of pump start-up/shutoff times, which were from 8 to 114 in different rainfall scenarios. Compared with the multistage pumping station optimization, the single pumping station optimization had a bigger number of pump start-up/shutoff times, which were from 1 to 133 times, and the pump operating time was also longer, from 72 min to 7542 min. Therefore, the multistage pumping station optimization method was more suitable to reduce the frequency of pump start-up/shutoffs.