In the era of ecological civilization construction, ecological compensation system is one of the most important systems among many environmental legal systems, which appears not only in the form of ecological compensation system policy, but also in the form of ecological compensation system law. Comprehensively reviewing the development process, current situation, and future development of the ecological compensation system, and examining from the dual perspective of policy and law, it can be found that the ecological compensation system has experienced a development process from pilot policy, legalization, to policy and law synergy. First, based on the adaptability and innovation of policy in gradual institutional change, the efficiency and diversity of policy under pragmatism, and the trial-and-error nature and flexibility of policy in the early stage of institutional implementation, the ecological compensation system is developed in the form of policy pilot, with policy as the basis. Second, through policy pilot, the ecological compensation system becomes increasingly mature, and gradually toward policy legalization. Examining the reasons, the policy legalization of ecological compensation system is the requirement and choice of inclusive system and system legalization. How to realize policy legalization of the ecological compensation system, specifically, a typed method needs to be adopted to divide policies into creative policies and implementing policies. Then through a two-way interaction mode, the top-down and bottom-up approaches can be taken for policy (creative policy) legalization. On this basis, the ecological compensation legislation in the future should be a systematic legal structure, including its basis in the Constitution, the ecological compensation system in comprehensive environmental protection law, special ecological compensation legislation, separate ecological compensation legislation and related ecological compensation legislation. Finally, according to the choice of formal institutional development under the new institutional economics and the requirement of mutual assistance and self-sufficiency of politics and law under the social system theory, the future development of the ecological compensation system inevitably need policy (implementing policy) and law synergy, to ensure its good operation. It is to meet the requirements of ecological civilization system construction, realize the dynamic development and constantly improvement of ecological compensation system, meet the needs of economic and social development, and enhance the adaptation of ecological compensation system.