Coordinated advancement of ecological environment damage compensation plays an important role in improving the ecological environment governance system and deepening the reform of the ecological civilization system. Currently, the ecological environment damage compensation system, which is centered on “public law rights, private law operations,” is essentially a system design under a private law governance model. However, it confuses the concept of state ownership of natural resources in the constitutional sense with that in the civil law sense, failing to fully meet the practical needs of ecological environment damage governance. To ensure timely and effective governance of ecological environment damage issues, the government must play a more critical role, and ecological environment damage governance urgently needs the strengthening of a public law governance model. Under the administrative leading public law governance model, the environmental administration’s performance is transformed into functional positioning with the unchanged obligations and performance methods, which fits the dual goals of effective governance and timely governance of ecological environmental damage. Looking forward to the future, the performance of environmental administrative agencies should be based on the particularity of ecological environmental damage, and follow the laws of administrative power as the follow-up rules of administrative power. It is constructed from the aspects of the scope of application, the determination of the subject, the process control, and the protection of rights. In addition, in cases where the person responsible for ecological damage cannot be determined, administrative agencies should bear the fallback responsibility using public financial funds. With the advancement of technology, once the person responsible is legally clarified, the public financial funds previously advanced should be repaid by the responsible party. For cases where ecological damage cannot be restored, administrative agencies should actively use their administrative powers to carry out alternative restoration work.