As an important component of terrestrial ecosystems, soil microbial communities are directly or indirectly involved in almost all soil ecological processes, including material cycles, energy conversion, and pollutant transformation. Studies of the spatiotemporal patterns of changes in soil microbial communities and the underlying mechanisms would help us determine the basic principle of microbial evolution, and would provide a scientific basis to predict the response, adaptation, and feedback of the microbial communities to environmental changes. In this review, we discuss the definition, analysis methods, and indices of soil microbial community. We argue that community could be the basic unit in macro-ecology and microbial ecology. Studies of community organization mechanisms are at the core of both the macro- and microbial ecology. Based on the community organization theories in ecology, ecological niche and neutral theories, process-based theories, and diversity-stability theories were introduced and applied to understand the soil microbial spatiotemporal patterns and the scale effects. A framework for the study of spatiotemporal patterns of changes in soil microbial communities was proposed based on the community organization theories under different spatial and temporal scales.