Soil aggregates are important components of the soil ecosystem. The formation and stabilization of soil aggregates affect the physical, chemical, and biological properties of soil; and play an important role in the formation of soil structure nutrients occurrence as well. Long-term application of organic fertilizer can increase soil organic matter content, provide cementing materials for the formation of soil aggregates, and promote the formation and stability of soil aggregates; which is one of the important ways to improve soil fertility and soil structure. To elucidate the effects of organic fertilizer on the formation and stabilization mechanism of soil aggregates, the responses of soil aggregate structural stability, carbon sequestration, nutrient occurrence, and microbial changes to these practices were summarized, and the relationships between organic fertilizer and different aggregate processes were discussed. Long-term organic fertilizer can accelerate the formation cycle of aggregates, enhance the stability of aggregates, increase the total amount of nutrients in aggregates,  and improve nutrient availability. The process and mechanism of soil aggregate formation and stabilization as well as the microbial driving mechanism of the nutrient accumulation process are still lack in research. Future investigation should strengthen multi-scale and multi-factor coupling studies in revealing the process mechanisms of soil aggregates under organic fertilizer application.