On the basis of generalizing the conception of river ecological compensation(eco- compensation) reasonably, according to river characteristics and people’s practice experience, the paper gives discussion on river eco-compensation mechanism from the angle of coupling system. By analyzing the characteristics during theoretical study and practical experience of river eco-compensation, to ameliorate the limitations, the paper describes the framework of effective river eco-compensation mechanism. For Xin'an River as an example, in the light of the present compensation theory, the author gives river eco-compensation mechanism overall framework based on co-construction and sharing ideas. Learning from the research progress and achievement of different areas, the paper gives typical examples analysis about trans-boundary river eco-compensation implementation on water quantity and quality joint operation level. Finally, the paper puts forward the improvement measures and further research emphasis of river eco-compensation.