Aiming at the characteristics of having higher fall of drain between the reservoir of water supply and that of water demand,and in order to resolve the problem of more generating surplus water of cascade hydropower station and low comprehensive efficiency of water receive reservoirs caused by unreasonable water transfer flow process in water delivery canal project,the paper put forward an optimal operation model of hydropower for two-dam water transfer project in Jinchang city which took the minimum volume of water shortage and the maximum hydropower as optimum goal.The paper used multi-objective genetic algorithm (MOGA) of Pareto strength to solve traffic diversion sequence Pareto, and analyzed operation rules of water supply reservoirs and water receive reservoirs in the framework of optimization，fitting and simulation based on optimal water transfer flow process. The result shows that the optimized operation scheme is reasonable and practice, and can improve the effectiveness of water delivery canal, increase the comprehensive benefits of water receive reservoirs and gain diversion and generation win.