Abstract: As vital territorial ecological spaces, national parks are tasked with balancing conservation and development. This mission imposes new requirements on the ecological compensation system. Based on the opportunity costs incurred by national park regulations and the need to promote green development, this paper proposes an analytical framework for binary logic ecological compensation. This study reveal that loss-mitigation compensation centers on offsetting opportunity costs, encompassing two approaches: resource conservation and conflict mediation. Incentive compensation, in contrast, aims to stimulate the endogenous motivation for eco-friendly behaviors, through two forms: behavioral guidance and project investment. Practices in China’s first batch of national parks demonstrate that loss-mitigation compensation is widely applied due to its standardized operations, whereas incentive compensation exhibits exploratory characteristics owing to its regional adaptability. From the perspective of binary logic, ecological compensation in national parks may face challenges such as structural imbalance, insufficient coordination, and simplistic evaluation. To address these issues, optimization efforts should focus on constructing a balanced structure, improving coordination mechanisms, and perfecting the evaluation system, thereby providing support for the integrated conservation and development of national parks.