The invention relates to a benefit compensation method and system for a cascade leading hydropower station. The system comprises a client layer, comprising a basic information management module, an optimization calculation module and a benefit compensation calculation module, a data server layer which is used for storing basic information data, dispatch calculation data and benefit distribution data and an external interface which comprises API, DBMS, URL and Web Service, wherein the basic information management module is used for managing and maintaining basic parameters and characteristic curves of the hydropower station, the optimization calculation module is used for calculating the increasing electricity output of the leading hydropower station in maximal cascaded generating capacity model for a downstream cascade hydropower station, and the benefit compensation calculation module is used for determining a final compensation benefit allocation method. The benefit compensation method and system for the cascade leading hydropower station consider not only conventional factors of hydropower station dispatching, but also the problem that a lot of river basins all face construction of large-scale water diversion projects, so that calculation results of the benefit compensation method are more comprehensive, and have broader practical values.