Conducting scientific research activities within nature reserves is beneficial for understanding the natural geographical environment, flora and fauna resources, biodiversity, and related threat factors within the protected areas. It is of great significance for evaluating the ecological benefits of nature reserves, protecting wildlife and plants, promoting harmonious development between humans and nature, and formulating plans and management measures. Unrestricted scientific research may not only waste costs, but also have negative impacts on the ecological environment within protected areas. It is necessary to regulate and adjust scientific research activities within nature reserves through scientific and reasonable administrative supervision measures to avoid the risk of institutional alienation. The existing legal and regulatory system lacks sufficient rules for the administrative supervision of scientific exploration activities within nature reserves, and there are conflicts and contradictions between different laws and regulations, making it difficult to achieve effective supervision of scientific exploration activities. Based on the existing institutional design and practical experience, and the inherent regulatory deficiencies of the independent approval mode of administrative agencies under administrative logic and the “notification entry” filing mode under scientific logic, a dual stage approval mode with the participation of expert review committees should be constructed under collaborative logic. Through the legislative improvement of the administrative supervision path, scientific investigation activities in nature reserves should be further regulated to reconcile the tension between administrative governance and scientific research.