For the operation problem of complex reservoir groups faced by the inter-basin water transfer project (IBWT) and its branch storage-regulation project (BSRP), taking the joint operation system consisted of the IBWT of Hanjiang to Weihe River and its BSRPs of Jiaoyan Reservoir and Yudaihe Reservoir as an example, the hydraulics and water yield connection between the water sources was revealed using topological generalization method. Then a joint operation model was constructed, and the long time series regulation of 10 years was solved by the collaborative particle swarm optimization (CPSO) algorithm. With this model, a multi-objective water supply scheme for an individual reservoir was proposed, and then the effect of IBWT and BSRP coupled system was analyzed. The results show that the BSRP can effectively increase the water supply and significantly improve the transfer process of the coupled system on the basis of balancing the multi-objective benefits.