Clarifying the spatial relationship and distribution pattern of protected area is the basis for strengthening spatial control as well as integrating and optimizing the protected area system. This paper conducted a case study on the protected area in Sichuan area of giant panda national park. Based on ArcGIS functions of processing, analysis and visualization of spatial data, the spatial relationship of various protected areas within the research region was quantitatively analyzed at the spatial level combining Venn diagram. The distribution pattern of giant panda (Ailuropoda melanoleuca) under different scenarios for conservation was further identified. The results showed that there were 6 types of protected areas in the study area, accounting for 75.13% of the total area, and 40.68% of which was overlapping region. Overlapping was widespread in all kinds of protected areas. Nature reserve accounted for 72.53% of the protected area as the biggest protected area type, of which 45.89% was overlapping. Other types accounted for 60.87% of the protected area, of which 66.48% was overlapping. A reverse growth trend was presented between the density of giant panda and overlapping level. In the protected area, the density of the non-overlapping region was higher than that of the overlapping. The Nature Reserve was the densest protected area, and its non-overlapping density was obviously higher than that of the overlapping region. The higher density occurred in the non-overlapping region of Forest Park and the overlapping region of Water Park. Among the protected areas that intersected with nature reserve, the density in nature reserve was much higher than that of the overlapping region. Thus, the original system of protected area had a large scope with complex spatial relationship in Sichuan area of giant panda national park. The conservation effectiveness between different regions was neither balanced nor sufficient. This paper suggests that the non-overlapping region of Nature Reserve, World Heritage within Nature Reserve, the non-overlapping region of Forest Park and the overlapping region of Water Park in the study area should be taken as the core protection zone for giant panda to protect strictly. The overlapping region of Nature Reserve and other region of World Heritage should be taken as the conservation zone to restore the damaged and degraded habitat of giant panda and its natural ecosystem. The region except above areas should be taken as general control zone, where human activities could be moderately carried out under the premise of effectively maintaining the giant panda population and its habitat. In addition, this paper proposes to carry out scientific evaluation for the overlapping, adjacent and junction region, and to clarify the unique attributes of the protected area. We also look forward to perfecting management system and the integrated planning of the spatial layout to promote the development of the protected area system composed mainly of the national park.