When carrying out conservation on key species in the protected areas, research on the conservation of similar species with their sympatric distribution is also of great value. On a larger geographical scale, the distribution area of black muntjac is completely covered by small muntjac. If we can grasp the overlapping status of the suitable habitats of them and reveal their coexistence mechanism, it will help to formulate conservation strategies and integrate management. From 2017 to 2020, the infrared camera technology was used to obtain 38 and 101 distribution sites of black muntjac and small muntjac, respectively, in Qingliangfeng National Nature Reserve, Zhejiang Province. Combined with 8 environmental factors, the MaxEnt model was used to predict the potential suitable habitats and analyze their overlap of black muntjac and small muntjac in the study area. The results show that: (1) the potentially suitable habitats for the black muntjac and small muntjac are mainly located in the southwest of Longtangshan area, the middle of Qianqingtang area and the northwest of Shunxiwu area, the mountains between Qianqingtang protection area and Longtangshan protection area, and the southern mountainous area of Shunxiwu. The total potentially suitable habitat areas are 586.66 km² and 661.93 km², and accounting for 36.67% and 41.37% of the study area, respectively. (2) The ecological overlap index of black muntjac and small muntjac is relatively high, the D value and I value are 0.82 and 0.97, respectively. Their total suitable habitat overlap area is 435.39 km², accounting for 74.22% and 65.78% of the total suitable habitat area for the black muntjac and small muntjac, respectively. (3) The selection of environmental factors between black muntjac and small muntjac is similar. Black muntjac mainly chooses the mixed coniferous and broad-leaved forests or broad-leaved forests with higher altitude, closer to water sources, and far away from settlements and roads, while small muntjac mainly prefers to select a mixed forest of coniferous and broadleaf forests with higher altitude, close to roads, far away from residential areas, and 500 m away from water sources. It is suggested to increase the establishment of ecological corridors among the various regions of Zhejiang Qingliangfeng National Nature Reserve and to strengthen further investigation and research on the distribution of black muntjac and small muntjac.