Soil microbes play an important role in a number of processes of the terrestrial ecosystem. Rapid urbanization brings about drastic changes in land use in urban and rural areas, thus forming a heterogenous environmental gradient, and directly and/or indirectly affecting compositions and functions of soil microbial communities and further on their ecosystem services. In the present review, composition characteristics of the soil microbial community varying with the landscape unit in the complex ecosystem and their main affecting factors, and functional variation of the soil microbial community along an urbanization gradient were summarized. An environmental gradient from urban to rural areas was found as a result of rapid urbanization causing variation of composition and functions of the soil microbial community. Land use, soil pollutants, vegetation cover, soil properties and some others were the main environmental factors jointly affecting soil microbial communities. However, the leading factors affecting soil microbial communities vary with the landscape. Then ecological service functions of soil microbes were discussed and their variation with the landscape analyzed. It is, therefore, essential to analyze further in detail effects of the social-economic-natural complex ecosystem, varying in characteristic and pattern, on soil microbial communities, to explore mechanisms of the generation and maintenance of ecological services that soil microbes in different functional zones of urban-rural complex ecosystem render to the soil, and to specify mechanism of soil microbes maintaining soil security and human health in a varying environment, so as to improve ecological service functions of the soil and maintain urban and rural soil security and health of the living environment.