In order to coordinate the water demand and contradiction of all parties in the water resources allocation system of South-to-North Water Diversion Project in Jiangsu Province, and improve the engineering efficiency and reduce the power consumption cost of the system, a multi-project and multi-objective joint optimization scheduling method was proposed. Based on this method, a joint optimization scheduling model was constructed, and a joint optimal scheduling scheme was proposed for three typical years of abundant, flat and dry water. Compared with the actual independent operation and dispatching mode of the North River Water Diversion Project and the East Route of the first phase of the South-North Water Diversion Project, the total power consumption cost of the joint optimal dispatching scheme can be reduced by 31%, 14% and 29%, respectively. Compared with the independent operation and dispatching mode, the joint optimal scheduling scheme can select and switch the water source and the water transmission route more scientifically, and make full use of the storage capacity of lakes along the route. Through the joint operation of complex sluice pump system, the mutual economy of different water sources can be realized, and the efficiency of the system can be improved more effectively.