The establishment of a national park system is pivotal for advancing ecological civilization in China, directly influencing the effectiveness of environmental governance. The issue of ecological protection compensation is closely linked to the effective implementation of this system during the establishment of national parks. This study delves into the policies, legislative characteristics, and practical experience of ecological protection compensation within China’s national parks, aiming to elucidate the system’s core principles and operational models. It is essential to adress practical challenges, including discrepancies between compensation standards and actual needs, the coordination deficits among compensation methods, and the inadequacies of the existing guarantee mechanisms within national parks. To achieve this, the paper proposes establishing scientifically-based compensation standards; enhancing coordination across various benchmarks; devising locally-adapted, comprehensive compensation methods; augmenting diversified funding mechanisms; delineating clear governmental responsibilities at all levels for ecological protection compensation, and bolstering horizontal compensation mechanisms. A comprehensive strategy is essential to develop an ecological protection compensation system for national parks based on the right to development.