Understanding the interaction between life history, demography and population genetics in threatened species is critical for the conservations of viable populations. In the context of habitat loss and fragmentation, identifying the factors that underpin the structuring of genetic variation within populations can allow conservationists to evaluate habitat quality and connectivity and help to design dispersal corridors effectively. In this study, we carried out a detailed, fine-scale landscape genetic investigation of a giant panda population for the first time, using a large microsatellite data set and examined the role of isolation-by-barriers (IBB), isolation-by-distance (IBD) and isolation-by-resistance (IBR) in shaping the genetic variation pattern of giant pandas in the Qinling Mountains. We found that the Qinling population comprises one continuous genetic cluster, and among the landscape hypotheses tested, gene flow was found to be correlated with resistance gradients for two topographic factors, rather than geographical distance or barriers. Gene-flow was inferred to be facilitated by easterly slope aspect and to be constrained by land surface with high topographic complexity. These factors are related to benign micro-climatic conditions for both the pandas and the food resources they rely on and more accessible topographic conditions for movement, respectively. We identified optimal corridors based on these results, aiming to promote gene flow between human-induced habitat fragments. These findings provide insight into the permeability and affinities of the giant panda habitat and offer important reference for the conservation of the giant panda and its habitat.