No direct or universal relationship was found between the aggregative factors induced by organic/synthetic input decomposition (binding molecules or decomposers of biomass) and temporal aggregate stability dynamics. This suggests the and can be improved by considering (i) the direct abiotic effect of some organic/synthetic products after the inputs, (ii) the initial biochemical characteristics of the organic/synthetic products and (iii) the effects of organic/synthetic products on the various mechanisms of aggregate breakdown. The application of synthetic fertilizers had no clear effect on SOC and N accumulation or their distribution in particle-size fractions. However, the combined application of pig manure and synthetic fertilizers enhanced the accumulation of SOC and N in all particle-size fractions, and led to a shift of SOC and N from fine to coarse particles. The application of synthetic fertilizers had no clear effect on SOC and N accumulation or their distribution in particle-size fractions. However, the combined application of manure and synthetic fertilizers enhanced the accumulation of SOC and N in all particle-size fractions, and led to a shift of SOC and N from fine to coarse particles. The paper reveals that the micro-aggregate protected C is promising for assessing the impact between manure and synthetic fertilizers long-term fertilization on SOC storage in conservation agriculture ecosystem of Typic Ustochrept soil.