Soil aggregation, mainly macro- (250–2000 μm) and micro- (53–250 μm) aggregates, directly affects the soil system i.e. pore size distribution, the microbial population, soil resistance to erosion, and resistance against degradation. Moreover, macro-aggregates play a significant role in soil organic carbon (SOC) storage and carbon sequestration. However, because macro-aggregates create an environment that facilitates interactions between clay particles and the SOC, protection by macro-aggregates becomes weak. Therefore, the direction of micro-aggregate formation is helpful for long-term soil carbon sequestration. This review suggests that the micro-aggregate protected carbon is promising for assessing the impact of agricultural soil conservation on organic carbon storage in soil. Soil degradation by agriculture practices leads to the destruction of the protective soil aggregate and soil structure. This exposes the labile carbon in these aggregates to microbial interaction. The present review found that SOC change was significantly influenced by organic inputs such as organic nanoparticles (CNPs), especially in sandy and clay soils poor in organic matter.