Protected area (PA) has been the cornerstone for conservation globally, but areas designated as protected may vary in their management and have overlaps between designations. China plans to establish a national park system for the first time, aiming to reform, integrate, and expand the existing PA system. However, there has been no comprehensive and 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 (GPNP) as an example, we analyzed the relationship between existing PA system and panda habitat, considering not only de jure designated PA coverage but also de facto levels of two types of potentially harmful activities (timber utilization and human disturbance). We find that, first, there are conservation gaps in the four mountains comprising the potential GPNP. Second, even currently PAs have management gaps in terms of restrictions on timber utilization and human disturbance. Third, overlapping of PAs appears to have adverse impacts on panda density. Based on these results, we propose integrated management under a single administration for the GPNP, focusing on the gaps and overlapping areas, especially key corridors connecting high panda population-density areas, which we identify. This study can serve as a reference for the establishment of other national parks in China and the world.