To address the mismatch between water demand of user groups and water transfer operation of hub groups in management of inter-basin water transfer projects, a “user-hub” group joint optimization and allocation model was developed, which balanced key operational indicators of hub projects in the water source region and multi-objective demands of users in the water-receiving region. In construction of the model, functional relationships among water resources, ecological environment, and socio-economic subsystems in the water-receiving area were quantified and nested in the water allocation model of the water supply subsystem, and multiple benefit objectives on water transfer, power generation, and energy consumption of the hub side were considered, so as to realize the optimal synchronization between water demand processes on the user side and water transfer processes on the hub side. The model was applied to the joint regulation simulation of the Hanjiang-to-Weihe Water Diversion Project in Shaanxi Province, and the results show that the joint optimization and allocation model enhances the overall operational efficiency of the inter-basin water transfer project, enabling flexible regulation of water demands and operational requirements of the “use-hub” group. Specifically, the water shortage rate of users is maintained at approximately 7%, with an increase of 3.6% in economic benefits. The reservoir group largely fulfills its water transfer tasks, achieving a total power generation of over 0.543 billion kW·h, with a reservoir vacancy rate maintained at around 8%, thereby reducing the risk of water shortages in the system.