The compensation for ecological environmental damage has experienced a development process from piloting to comprehensive promotion, and its theoretical research and practical exploration are constantly enriched and improved. In the process of system reform, some key issues need to be clarified, such as the basis of claim right for compensation, the identification of the nature of compensation negotiation, the procedural connection between compensation negotiation and compensation litigation, and the coordination between compensation litigation and environmental public interest litigation. Therefore, we should explore the proper orientation of compensation for ecological environmental damage from multiple perspectives, such as system function, attribute and efficiency. The development and reform of the compensation system for ecological environmental damage should pay attention not only to the formulation of substantive rules, but also to the scientific design of procedures. We should strengthen the construction of the compensation system for ecological environment damage, and promote the overall construction of the damage relief system. In addition, we should pay attention to the improvement of internal control mechanism and external supervision mechanism.