Ecological environment governance is a complex system engineering. Based on the analysis of the multiple co-governance of the ecological environment in the yuanshui river basin, it is shown that the multi-governance bodies such as the government, enterprises and the public begin to interact and integrate with each other in the ecological environment governance of the yuanshui river basin, but there are still difficulties in the goal of ecological governance, the structure of ecological governance and the operation of ecological governance. To form the multi-governance mechanism, we need to strengthen the government guidance mechanism, improve the market regulation mechanism and straighten out the public participation mechanism.