The sustainable development of agriculture is one of the key bases of continuous prosperity of human civilization. During the progress from primitive farming to industrial agriculture, the influences of "natural force" decreased but those of "anthropogenic regulation force" increased. The oncoming sustainable agriculture aims to integrate the two forces to establish a modern farming system which is expected being characterized by both close-to-nature and high efficiency. However, the conventional reductionism approach fails to fully explore the natural processes in belowground ecosystems due to their extremely high biodiversity, complex biotic and/or abiotic interactions, and great spatial and temporal heterogeneity. Consequently, it is difficult to develop a precision agricultural management to regulate a specific process successfully. Nevertheless, the critical contributions of soil biota to ecosystem services have now been universally recognized. It is an important cutting-edge research field of modern agriculture to fully improve the positive influences of soil biota on sustainable agriculture. In this study, we outlined the history and state-of-the-art in studies of soil biota and sustainable agriculture, summarized the impacts of agricultural management practices on the characteristics of soil biota and soil food webs. We emphasized the critical roles of soil biota community in sustainable farms for improving soil structure and soil fertility and reducing applications of chemical fertilizers and biocides. Finally, the research challenges and prospective research fields as well as the framework of improving the performance of soil biota in the modern farming systems were discussed. We considered that the key aspects in sustainable agriculture studies are soil organic matter, soil structure and soil food web, as well as the inherent connections among them. While the management of soil organic matter is the base and key point in regulating soil structure, soil food web and ecosystem productivity, however, it is also one of the most important uncertainty sources in sustainable farming. The systematical investigation of soil food web characteristics and their ecological functioning in representative agricultural ecosystems, based on application of holistic approaches such as isotope tracing, are needed. Thereby, the key connections among agricultural mode, soil food web characteristic and ecosystem productivity could be explored, and thus, the potential contributions of soil biota to sustainable agriculture could be fully stimulated.