Soil aggregates are the essential building blocks of soil, which impact the retention and distribution of water, air, heat, and nutrients. Binding materials play a pivotal role in the formation of soil aggregates. However, the specific functions of different types of binding materials as well as the mechanisms of the complex interactions in the formation of these aggregates still lack a systematic summary. This article reviews the key theories related to soil aggregates and sorts out types, forms, transformations, and interaction mechanisms of binding materials in soil aggregates under different geographical contexts and human activities. It also describes the effects of binding materials (e.g., organic matter, minerals, roots, organisms and their derivatives such as Extracellular Polymeric Substances) on the structure and stability of soil aggregates. Furthermore, it introduces models illustrating the self-organization process driven by binding materials within soil aggregates and elucidates the mechanisms of the formation and transformation of soil aggregates. Finally, the future development of soil aggregates is suggested. Specifically, future research could investigate the in-situ analysis of soil aggregates, quantitative description of the formation process of soil aggregates, spatial structure of soil aggregates at the landscape scale in relation to its stability, and development of product/technology in cultivating good soil aggregates for applications. This research holds significant scientific and practical value in promoting the development of healthy soil aggregates, unraveling the processes of soil elemental cycling and evolution, and enhancing overall soil quality and productivity.