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The construction and operation of cascade reservoirs has changed the natural hydrological cycle in the Yalong River Basin, and reduced the accuracy of hydrological forecasting. The impact of cascade reservoir operation on the runoff of the Yalong River Basin is assessed, providing a theoretical reference for the construction and joint operation of reservoirs. In this paper, eight scenarios were set up, by changing the reservoir capacity, operating location, and relative location in the case of two reservoirs. The aim of this study is to explore the impact of the capacity and location of a single reservoir on runoff processes, and the effect of the relative location in the case of joint operation of reservoirs. The results show that: (1) the reservoir has a delay and reduction effect on the flood during the flood season, and has a replenishment effect on the runoff during the dry season; (2) the impact of the reservoir on runoff processes and changes in runoff distribution during the year increases with the reservoir capacity; (3) the mitigation of flooding is more obvious at the river basin outlet control station when the reservoir is further downstream; (4) an arrangement with the smaller reservoir located upstream and the larger reservoir located downstream can maximize the benefits of the reservoirs in flood control.