Abstract:Constructing a natural reserve system is one of the most effective measures to protect biological diversity. Species diversity is an intuitive understanding of biological diversity and an essential criterion for measuring the richness of regional biological resources. To evaluate the protection effect and optimize the spatial layout of Chongqing’s natural protected area system, this paper first established the spatial data of Chongqing’s natural protected areas on the ArcGIS platform. Secondly, the distribution data of plant species within Chongqing City were collected, and the MaxEnt tool was used to establish the maximum entropy model of the distribution of each indicator species. Then, the species richness evaluation tool will superimpose each species distribution model to obtain the species richness index. Finally, it was compared with the existing natural protected area system in Chongqing to evaluate the effectiveness of its protection, identify gaps and deficiencies, and put forward suggestions for natural protected area planning. The study found that Chongqing’s nature reserve system only protects 9.12% of the areas with high species richness, and the protection gaps are concentrated in mountainous areas such as Daba Mountain and Wushan in northeastern Chongqing and Wuling Mountain in southeastern Chongqing. It is recommended that the scope of existing protected areas in the areas mentioned above be expanded, natural protected areas are added, and the coordinated management of cross-administrative natural protected areas be strengthened.