Protected natural areas play an important role in biodiversity conservation and environmental quality improvement. However, its spatial boundary conflict results in a weak control, with the contradiction between protection and development to be further solved. Therefore, by using GIS spatial superposition analysis technique, an analysis has thus been made of the spatial pattern as well as spatial conflict characteristics of the protected natural areas in Zixing City, followed by a comprehensive evaluation of its spatial homogeneity. The results show that 5 of the 6 protected natural areas in Zixing City are characterized with one or two overlapping, covering a total area of 29 577.30 hm2. Therefore, by adopting such spatial reconstruction measures as the integration of overlapping areas and boundaries, functional integration and management and control zoning, the protected natural areas in Zixing City are classified into two categories and four places, with the total area of the protected areas increasing by 0.02% compared with what prior to integration and optimization. Meanwhile, the corresponding management structure should be integrated and differentiated management and control should be implemented to realize the "one map" management and control of land and space planning.