Background: Religious sites are carriers of religious culture communication, reflecting the types, development history and influence space of religions. However, the construction of religious sites in different historical times and different regions is affected by many factors. This study explores the spatial distribution characteristics and influencing factors of religious sites in Inner Mongolia under the influence of many factors, so as to provide reference for understanding the spread and influence of religion in different time and space. Methods: In order to show how religious sites are affected by these factors, this paper uses GIS to extract the relevant factor data of religious sites and analyze the relationship between the number of other religious sites. Results: Although religious sites were constructed at different historical times, it can be inferred according to the existing data that the religious sites are affected by the terrain, elevation, landscape, river, and lake conditions. At the same time, the religious sites are also restricted by the population and economic scale. The number and growth of religious sites show a certain regularity in different historical times. Conclusion: The distribution of religious sites in Inner Mongolia presents the characteristics of dual core distribution, and different religious types also have significant differences in the choice of cities and rural areas, mountains and plains, rivers, and lakes; religious sites are closely related to the local population, economy, and historical time.