The use of engineering procurement construction (EPC) mode is currently a trend in hydropower engineering construction. The clarification of the internal relationship between hydropower EPC projects and the realization of synergy has great significance in improving management efficiency and implementation effect. In this work, a three-dimensional system and a system model of hydropower EPC project management synergy are constructed. The mechanism and factors that influence the degree of management synergy are analyzed on the basis of management synergy theory. Furthermore, the evaluation index system and the degree of synergy model are established, and grey relational analysis is utilized to identify the key factors that affect the synergy degree. Thus, this study aims to facilitate the hydropower EPC project management synergy, provide a quantitative method for synergy degree evaluation, and propose corresponding promotion strategies. Results show that the order degree of each subsystem presents a steady upward trend. Specifically, the order degree of the subsystem at the trial operation stage is low, which is the major restriction on the further improvement of the synergy degree of EPC project management. The key factors in improving the synergy level of hydropower EPC project management are mainly concentrated in the information and organization synergy subsystems, including the construction degree of information platform, the performance of functions, the timeliness of information transfer, and the functions of the information platform.