Based on the entropy generation theory, the hydraulic loss of each component of the pump-turbine is analyzed, and a local coordinate system analysis method is proposed to quantitatively analyze the spatial local loss of the runner under multidimensional conditions. The research results show that, under the operating conditions in the hump region, the hydraulic loss contributed by indirect entropy generation is the highest, accounting for 71%, the hydraulic loss contributed by direct entropy generation is the lowest, accounting for only 1%, and the hydraulic loss contributed by wall surface entropy generation accounts for 27%. The flow separation phenomenon at the runner inlet blade develops into separation vortices, leading to backflow near the shroud region, and a backflow phenomenon occurs in part of the vaneless area, resulting in a significant increase in indirect entropy generation. The decrease in head in the hump region is closely related to the significant increase in hydraulic loss, which is greatly influenced by the backflow effect near the runner inlet and in the vaneless area.