The Northeast Sika deer is one of the major large herbivores in the Northeast Tiger and Leopard National Park. It is the main prey of the Amur tigers and leopards. It also plays a key role in maintaining the coniferous and broad-leaved mixed forest community. It is very important to explore its genetic diversity and the spatial genetic pattern for conservation of the Sika deer and the ecosystem of the national park. In this study, genetic samples were obtained by non-invasive methods in Hunchun Reserve in the National Park, and microsatellite markers were used to study the spatial genetic pattern of the sika deer population and its influencing factors. The results showed that the average expected heterozygosity of the sika deer population was 0.721, which was rich in genetic diversity compared with other populations. Limited dispersal capacity often results in populations with significant spatial autocorrelation patterns over genetic distance. The sika deer population had the significantly spatial autocorrelation in the genetic distance of 0—1 km distance grade, based on which it could be speculated that the sika deer dispersal distance or home range was about 1 km. STRUCTURE analysis showed that there was no significant genetic differentiation in the population.Various spatial variables can significantly influence the genetic differentiation of species. In this study, 5 variables, altitude, slope, slope, surface relief ratio, and human disturbance, were selected to study their effects on the genetic structure of the population, which are mostly considered to be associated with dispersal barriers in large and medium-sized mammals. This study built 336 resistance models based on those variables and performed the partial Mantel test. Among them, 246 resistance models based on the hypothesis of altitude, slope, surface surface relief ratio, and human disturbance were not significantly related to genetic distance, nor were the 15 habitat suitability models integrating all variables. Of the 75 resistance models constructed under the slope hypothesis, only 1 model showed significant positive correlation with genetic distance, which was also the model with the highest correlation with genetic distance among all models after controlling for spatial autocorrelation effects. According to the model, the most suitable slope for sika deer dispersal is 10°, sika deer may tend to use gentle slope for dispersal. The results were important for the conservation of sika deer populations in the National Park.