With increasing emphasis on ecological environment conservation, the conservation of fish habitat and the regional carbon balance need to be incorporated into the operation process of reservoirs. In this research, formulas for calculating ecological and environmental objectives in reservoir operation were obtained by fitting the curve of discharge and fish habitat area and comprehensively analysing the factors affecting reservoir carbon emissions. Additionally, we used the multi-objective optimization algorithm NSGA-II-DE to study the competitive relationship between the economic, ecological, and environmental benefits of the Longtoushi Reservoir and proposed a relatively optimized operation scheme using the multi-objective decision-making method VIKOR. The results of this scheme showed that the power generation, weighted usable area (WUA) and carbon emissions of Longtoushi Reservoir during the study period were 5.74 × 108 kW h, 9.61 × 104 m2 and 51.32 t, respectively. Compared with the relative optimal operation scheme, the power generated by the maximum power generation scheme increased by 2.66%, the WUA decreased by 1.68%, and carbon emissions increased by 9.86%; the power generation of the maximum WUA scheme increased by 0.16%, the WUA decreased by 0.08%, and carbon emissions increased by 0.72%; and the power generation of the minimum carbon emission scheme increased by 3.14%, the WUA decreased by 1.62%, and the carbon emissions increased by 9.14%. In general, competition between power generation, WUA and carbon emissions is inevitable, and reducing the water level in reservoirs can effectively increase ecological and environmental benefits.