There is potential competition between roe deer (Capreolus pygargus) and sika deer (Cervus nippon), and investigating on the overlap of their ecological niches is of guiding significance for the management of nature reserves. Using data from 66 infrared camera traps deployed in 2021 across the Liancheng National Nature Reserve in Gansu Province, combined with eight environmental variables, we employed the Biomod2 modeling and kernel density estimation methods to predict potential suitable habitats for roe deer and sika deer within the reserve, as well as to analyze their temporal and spatial niche overlap. The results showed that: (1) The two species exhibited similar environmental preferences. Roe deer tended to occupy areas with higher annual precipitation, higher elevation, and greater distance from roads, whereas sika deer tended to occupy areas with greater distance from residential location, with high annual precipitation and greater distance from roads. (2) The suitable areas of the roe deer and the sika deer were mainly located in the central and western parts of Tanggou, the southern part of Zhulingou, the northern and southern parts of Zhinanbei, Tianwanggou, and the eastern part of Minle, and the high suitability habitat area of roe deer was larger than sika deer, and the total overlap of their habitat area was 137.60 km2, accounting for 87.19% and 49.58% of their total habitat area, respectively. (3) Temporal niche overlap was high, with both species showing crepuscular activity patterns. During the warm season, roe deer increased their activity during periods of low sika deer activity, likely a strategy to reduce interspecific competition and meet survival needs. But in the cold season, due to the scarcity of resources and the cold climate, both of them exhibited intense activity competition in the afternoon. This study investigated the spatial and temporal ecological characteristics and overlap between roe deer and sika deer, which can provide a reference for animal protection departments in the conservation of deer populations and the restoration of their habitats.