In traditional ecological operation, it is difficult to coordinate the balance among the interests of stakeholders, and stakeholders find it difficult to accept the operation scheme. To address these problems, this study proposed a method of multi-stakeholder coordinated operation of reservoir (MSCOR). By comprehensively considering the interest demands of stakeholders, the multi-stakeholder interval coordination mechanism (MSICM) for reservoir operation was established. The multi-stakeholder coordinated operation model (MSCOM) was constructed. The multi-stakeholder solution algorithm based on the MSICM, the non-dominated sorting genetic algorithm II, and the approach of successive elimination of alternative schemes based on the k-order and p-degree of efficiency (MSIC-NSGA-II-SEABODE) were applied to solve the MSCOR problem. The coordination mechanism, model construction, multi-stakeholder optimization, and multi-attribute decision making were coupled to establish a multi-stakeholder coordinated operation method, comprising the whole process of mechanism–modeling–optimization–decision making. Taking Baojixia Reservoir as an example, the performance of the coordinated operation method was compared with that of the traditional optimal operation method, and the relationship between the irrigation benefits and ecological benefits of the reservoir was explored. The results show that: (1) On the premise of the same satisfaction degree of basic irrigation interests, the ecological AAPFD value of coordinated operation decreased by 0.184, 0.469, and 0.886 in a normal year, dry year, and extraordinary dry year, respectively. The effect of coordinated operation on balancing various stakeholders was more obvious with the decrease in water inflow. (2) The MSICM ensures that the multi-stakeholder operation of the reservoir conforms to the principles of comprehensiveness, balance, and sustainability. (3) The coordination scheme obtained by the MSIC-NSGA-II-SEABODE algorithm is more reasonable and feasible. The research results provide a new idea and method to address the MSCOR problem.