Abstract: The indivisibility of the eco-environmental system requires the integrity of the eco-environmental governance. At present, the construction of ecological civilization in my country emphasizes the construction of “large environmental protection” . Cross-regional ecological governance is an important part of the construction of ecological civilization, it emphasizing the systematic and holistic governance of the ecological environment. The holistic governance theory provides a comprehensive analysis framework for cross-regional ecological governance from four levels: governance concept, organizational structure, operating mechanism and technical system. The article analyzes the dilemmas faced by cross-regional ecological governance in China, including the backward governance concepts, fragmented organizational structure, urgent needs to improve operating mechanisms, and flaws in technical systems.It emphasize to solve the problems of the cross-regional ecological governance and promote the practice of the cross-regional ecological governance by updating governance concepts, adjusting organizational structures, innovating operating mechanisms, and optimizing technical systems. Cross-regional ecological governance to improve the living environment and build a beautiful China.