Hydropower is an essential resource for the future clean energy transition, in which an accurate assessment of the hydropower cost is vital for promoting its share in the energy market. The purpose of this paper is to comprehensively reassess the cost of hydropower from a new perspective, in which the total static investment cost of a hydropower base is allocated among multiple functions. An allocation coefficient is proposed based on indicators of economic value and physical volume of multi-function hydropower bases. The economic value of each function is evaluated using approaches including the shadow project, market valuation, and emergy evaluation methods. Meanwhile, the physical volume is obtained through a multi-objective optimization of cascade reservoir operation considering an ecological constraint. Four main functions consisting of hydropower generation, flood control, agricultural irrigation, and residential water supply of hydropower bases in Sichuan are investigated. The results show that the allocation coefficients under both economic and physical indicators vary significantly among hydropower bases, and change slightly over the years. The average comprehensive allocation coefficient of hydropower is 57.26% (range from 29.83% to 77.41%), and the hydropower cost can be reduced by 59% from the current level. The reassessed hydropower cost can lay a solid foundation for market pricing. Attention should be paid to the multi-functionality characteristics of hydropower bases to achieve fair sharing of cost and benefit.