Urbanization brings economic prosperity while causing environmental problems, and as a greening landscape of the urban ecological environment, the urban trees also have the function of alleviating these problems. As the growth environment of urban trees, the health status of soil environment directly affects the growth status of urban trees, and soil microorganisms are important biological communities in soil ecosystems, which maintaining urban ecological functions together with urban trees. Among soil microorganisms, soil bacterial and fungal communities in the surface layer of soil can react quickly to environmental changes, and they can therefore be used as indicators for measuring the impact of environmental changes. The purpose of this study was to explore the differences in response of soil bacterial and fungal communities along urban-rural environmental gradients, and a total of 7 Styphnolobium japonicum (L.) Schott trees in Beijing were selected as research samples, and then its rhizosphere soil were excavated for soil microbial determination so we can explore the differences in response to urbanization in community composition and species diversity of soil bacterial and fungal communities, and finally identify environmental factors that affect their distribution. The results showed that: (1) The distribution and composition of soil microbial communities will be affected by urbanization, specifically manifested by significant differences between soil bacterial and fungal communities in urban-rural environmental gradients, and a total of 41 categories of soil bacteria were detected, among which Actinomycetes, γ-Proteobacteria, Bacteroides, Myxococcus, and Firmicutes were significantly different in the urban-rural gradient, and a total of 16 categories of soil fungi were detected, among which Basidiomycetes and Rozellomycota were significantly different in the urban-rural gradient. (2) Environmental factors that affect the distribution of soil microbial communities include soil physicochemical properties and climatic factors, and environmental factors affecting the distribution of soil bacterial communities include soil pH, soil organic carbon, soil total nitrogen, and mean annual temperature, while environmental factors affecting the distribution of soil fungal communities include soil organic carbon, soil total nitrogen, soil total phosphorus, and mean annual precipitation. (3) Among areas affected by urbanization, the suburb is the area affected by urbanization mostly, and the composition of soil bacterial communities in the suburbs has a certain degree of overlap, while soil fungal communities can be completely separated across the entire urban-rural gradient. (4) The soil bacterial communities are more susceptible to environmental factors than soil fungal communities on the urban-rural gradient, and their environmental sensitivity is higher.