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.　©　2016,　Editorial　Board　of　Journal　of　Systems　Engineering　Society　of　China.　All　right　reserved.