Protected areas have been the cornerstone for conservation globally [1], but gaps still exist in preserving biodiversity [2]. Meanwhile, areas designated as protected have overlaps between designations and might vary in their management [3, 4]. All three phenomena—coverage gaps, overlapping designations, and disparities in management—are present in China [5, 6]. China plans to establish a national park system for the first time, aiming to reform the existing protected-area system [7, 8, 9]. However, there has been no quantitative spatial analysis that can aid the planning of national parks. This study shows how an improved conservation gap analysis can inform the construction of new national parks. Taking the proposed Giant Panda National Park as an example, we analyzed the relationship between panda habitat and the existing protected areas, considering not only de jure designated coverage but also de facto levels of two types of potentially harmful activities (timber extraction and human disturbance). We find that, first, there are coverage gaps in the four mountains comprising the potential national park, and existing protected areas have overlaps between designations. Second, current protected areas have gaps and disparities in terms of restrictions on timber extraction and human disturbance. Third, overlapped designations and less restrictive management appear to have adverse effects on panda protection. On the basis of these results, we propose integrated management under a single national park administration, focusing on the key gaps, which we identify. This study can serve as a reference for the establishment of other national parks in China and the world.