Soil aggregates are an important component and basic unit of soil structure, and their stability is crucial for maintaining soil health and crop productivity. The formation and stability of aggregates are the result of the joint action of biological and non-biological factors, and soil organisms (microorganisms and animals) play a crucial role in this process. A thorough understanding of the relationship between soil organisms and the formation and stability of aggregates is of great theoretical significance in elucidating the process and mechanism of soil quality change. However, systematic summaries of the driving mechanisms and current application status of soil organisms in aggregate formation and stabilization are still lacking. This paper reviews the effects of soil microorganisms and animals on aggregate formation and stabilization and clarifies the aggregate formation process and stabilization mechanisms driven by soil organisms. The study discovers that microorganisms mediate aggregate formation and stabilization through their physical characteristics, secretion of adhesive substances, and decomposition of organic matter, while animals mediate aggregate formation and stabilization through biological disturbance and feeding. Furthermore, the current status of using soil organisms and their products to increase aggregate stability is analyzed, emphasizing the potential application of novel soil biological structural modifiers. In conclusion, prospective research directions are outlined for future investigations. Researchers should concentrate on the following areas: (1) The formation and stabilization mechanism of soil aggregates driven by soil organisms on multi-scale interface processes; (2) The composition and genetic regulation mechanism of microbial extracellular polymeric substances (EPS) and glomalin-related soil protein (GRSP); (3) The influence mechanism of soil archaea and viruses on the formation and stability of aggregates; (4) The formation process and stabilization mechanism of aggregates mediated by soil food web; and (5) Development and application of biological soil structure improvers. This paper aims to provide both theoretical insights and technical guidance for maintaining and improving soil quality.