The compensation for ecological environment damage in China started from the governance of the Yangtze River and the Yellow River cross-administrative regions. It has undergone reflection and exploration of the practice of the ecological compensation system across administrative regions, establishing a mechanism for resolving disputes over the ecological environment at the source of the river basin. Regarding the approaches to resolving disputes over water pollution in cross-regional river basins, the legal assertion advocates a combination of negotiation and coordination. The Civil Code stipulates that the new rules of the punitive compensation system should be applied to ecological environment infringement. To construct a complete system of litigation for compensation for ecological environment damage, it is necessary to establish a government claim litigation system for ecological environment damage, establish a pre-litigation procedure as the paradigm for procuratorial organs to perform public interest litigation in the environmental field, and standardize the collaborative model of the compensation system for ecological environment damage. To improve the judicial application system for punitive compensation for torts, it is necessary to construct a civil public interest litigation system for punitive compensation for ecological environment damage, a civil application system for punitive compensation for criminal attached civil public interest litigation cases, and a judicial application system for punitive compensation for ecological environment tort cases.