Abstract: The clusters of inter-basin water transfer pumping stations are a vital power source to address the spatial imbalance of water resources distribution. Despite their significant comprehensive benefits, the increasingly prominent issue of high-water transfer costs necessitates further investigation into the economical operation of pumping stations. This study develops a daily optimization scheduling model for parallel pumping stations with dissimilar units, taking into consideration time-of-use electricity pricing. By optimizing the control periods and flow distribution of the units, the model aims to achieve the economical daily operation of parallel pumping stations. The Suining Hub Station of the East Route of the South-to-North Water Diversion Project is taken as a case study to analyze the optimized flow distribution pattern and the response of water transfer cost to the number of control adjustments. The results indicate that under the designed head, primarily the Suining No. 2 station units adapt to the changes in water transfer flow; under fixed flow conditions, it is mainly the Shaji Station units that accommodate the changes in pumping station head. With a fixed number of control adjustments, time-of-use electricity pricing better unleashes the potential of scheduling compared to fixed electricity pricing. Under time-of-use pricing, increasing the number of daily control adjustments can save more costs, albeit the extent of savings is limited by the constraints.