The Red Deer (Cervus elaphus) plays an important role in ecosystem function in northeast China, but their populations had seriously suffered from habitat degradation and human disturbance. In this study, we investigated the population recovery and habitat status of red deer by means of line transects and pellet group counting methods in southern part of the Greater Khingan Mountains, Inner Mongolia. The results showed that after 10 years’ development, the population density increased significantly in Huanggangliang, Baiyin’aobao, Dalengshan, Saihanwula, Wulanba and Gaogesitai areas (P < 0.05). The total number of red deer in the study region was about 9 644.2 ± 1 378.6 ind, and the population density was 2.5 ± 0.9 ind/km2. This study provided solid baseline data for red deer conservation in the southern part of the Greater Khingan Mountains, and we further discussed the measures to promote a steady recovery of the red deer population according to habitat restoration and population management.