Aiming at the problem of joint optimal operation at the five hydropower plants of Three Gorges and Qing River cascades, the paper adopts three-class structure to decompose and coordinate the optimal problem, which takes the maximum system power benefit as the optimization criterion under considering the flow propagation and the variable price factor. This paper derives the iterative formula of decomposition coordination method and identifies the convergence conditions of problem. The study case of Three Gorges and Qing River cascades in different conditions shows that total output of joint optimal operation is bigger than that of cascade single operation. Three Gorges and Shuibuya with large capacity of regulation, have larger output in power systems correspondingly when inflow is the same. In addition, this method is also effective in reducing the resolving time of giant hydropower stations optimal operation and improving the operational efficiency.