Historically, giant panda conservation in China has been compromised by disparate management of protected areas. It is thus crucial to address how giant panda populations can be managed cohesively on a landscape scale, an opportunity offered by China’s newly established Giant Panda National Park. Here, we evaluated giant panda populations in a metapopulation context, based on range-wide data from the Fourth National Giant Panda Survey. We delineated metapopulations by geographic range, relative abundance, and relative density and assessed the extent of human disturbance each metapopulation faced. We found density-dependent and disturbance-influenced effects on habitat selection across metapopulations. We determined the main effects faced by each metapopulation regarding area sensitivity, population size, intraspecific competition, and disturbance. To enhance the landscape-scale conservation of giant pandas and various other wildlife across China’s national park system, we propose that metapopulation management incorporates population status along with density-dependent and disturbance-related effects on habitat selection.