Habitat fragmentation is one of the main causes of species endangerment. Functional zoning is an important means of spatial distribution planning and conservation effectiveness improvement. Habitat suitability evaluation is an essential measure to improve the function of the protected areas and guide rational zoning. Focusing on the existing problems in the protected area function zoning, namely, inconsistency with the spatial pattern of suitable habitat, lacking close connection with surrounding areas, and enhancement edge effects, this study took Duoer National Giant Panda (Ailuropoda Melanoleuca) Nature Reserve in Gansu Province as an example. According to the landscape characteristics of the existing protected area zoning, the functional zoning of the protected area should be adjusted based on improving the integrity and connectivity of the suitable habitats by expanding the study scale and carrying out habitat suitability evaluation, combining the heterogeneity of the suitable habitat and the landscape characteristics of the functional area. The effectiveness of the method used in the study was evaluated by comparing the changes of landscape characteristics and habitat suitability before and after regionalization and the space utilization of giant panda. Results shows that the suitability evaluation based on this method was effective. The suitable habitat in the core area of the new zoning increased by 16.03%, the protected quality habitats increased. The inner margin ratio of the core area decreased from 5.35 and 6.32 before adjustment to 3.97, the protected high-quality habitat increased, and the edge effect significantly decreased, which improved the integrity of the suitable habitat of the reserve and strengthened the connection with the surrounding high-quality habitat. It can help improve the environmental capacity of the core area, enhance the ability to resist external disturbance, improve the living conditions of giant pandas and promote the regional population exchange.