The mathematical model of optimal daily operation with variable speed for multiple pump units in single pumping station was constructed by taking the minimal daily electric cost as objective function. Considering the efficiency of variable frequency drive (VFD) varied with the unit rotational speed, the decomposition-dynamic programming aggregation method was applied to solve the model above. Taking minimal daily electric cost as objective function, the water quantity pumped by units as coordinated variable, this model was decomposed into several sub-models of daily optimal operation with variable speed for single pump unit. The constructed aggregation model took water quantity pumped by each pump unit as decision variable, the discrete values of water quantity pumped by pumping station as state variable. Both sub-model and aggregation model were solved by means of dynamic programming method. The decomposition-dynamic programming aggregation method could solve the optimal variable speed operation issues for multiple pump units with different types or the units of the same type with performance differences in single pumping station. Through the study on the operation of No.3 Huaiyin Pumping Station which is the third stage pumping station of South-to-North Water Diversion Project in China, a series of optimization results were obtained.