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According to the problem of traditional CCR model and two-stage DEA model in eco-efficiency measurement, this paper proposes a new two-stage model based on cooperative game, and applies to evaluate eco-efficiency of production system, which has complicated internal structure and undesirable outputs. Then, this paper constructs an efficiency decomposition model based on optimal coordination efficiency to solve the problem that subsystem efficiency may not be only, and finds the influencing factors of efficiency from a deeper level, in order to promote two subsystems common development. Finally, an empirical case about water eco-efficiency of regional industrial system in China is introduced to verify the rationality and validity of the model in this paper. [ABSTRACT FROM AUTHOR]