The invention relates to a multistage pumping station water transfer project station discarding optimization scheduling method comprising the steps that station discarding feasibility analysis is performed on the pumping station; whether station discarding can be performed is judged; a station discarding operation feasible region is formed; a station discarding optimization scheduling model is constructed; the scheduling result is optimized; a station discarding regulation and control model is constructed; and a station discarding regulation and control scheme is formed. The station discarding optimization scheduling method suitable for the multistage pumping station water transfer project under the low flow water delivery condition of the specific period (the project trial operation period or less available water supply of the water source region) is established so that the number of pumping stations participating in water transferring can be optimized according to the actual condition and the operation cost can be reduced; meanwhile, the operation condition of the pumping stations adjacent to the discarded station is also optimized, and the pumping station lift is reasonably allocated so that further energy conservation and consumption reduction can be realized and the scientific basis and the technical support can be provided for actual scheduling.