The hydropower project had comprehensively benefited people from aspects of the economy, society, ecology, etc. The comprehensive benefit is a key indicator for evaluating a project’s performance. However, the existing studies only evaluated the comprehensive benefit and ignored the relationship among different benefits, which is of great significance for the sustainable development of a project. Therefore, in the framework of the complex system composed of economic, social, and ecological benefit subsystems, a synergy degree evaluation method is constructed based on the evaluation index system of the comprehensive benefits, and the compound weight is determined by using the non-linear model and the Lagrange function. Thus, the changing rules of the order degree and the synergy degree for the subsystems in different years can be obtained. The proposed method is applied to a gate dam (named SG) to appraise the relationship among benefits. The results show that the economic, social, and ecological benefits of the SG dam from 2011 to 2018 are gradually to be a better state, but the synergy degrees of the complex system belong to “bottom synergy” and “moderate synergy” level, which indicates that there is no close cooperation among the three benefit subsystems.