This study aims to present a joint operation framework for complex multiple reservoir systems to balance water supply between subsystems and between different stakeholders, and support decisions about water releases from the entire system and individual reservoirs effectively. The framework includes three steps: (1) aggregated virtual reservoirs and various subsystems are established to determine the water releases from the entire system; (2) the common water-supply strategy is identified to determine the water releases from individual reservoirs; and (3) the joint operation problem is solved with a multi-objective optimization algorithm and the results are analyzed using a Many-Objective Visual Analytics Tool (MOVAT). A case study of the DaHuoFang-GuanYinGe-ShenWo multi-reservoir system in northeastern China is used to demonstrate the framework. Results show that the establishment of aggregated virtual reservoirs and identification of a common water-supply strategy could make use of the temporal and spatial differences of runoff, exert the effects of underlying hydrological compensation between river basins, and reduce the complexity of the joint operation model for multiple reservoir systems effectively. The MOVAT provides an effective means of solving many-objective problems, which are generally of particular concern to the decision-maker in practice.