In the context of global climate change, the preservation of soil productivity and the estimation of carbon budgets and cycles, the quantification of changes in carbon has important significance. In this study, we investigated the dynamics of soil aggregate associated organic carbon (OC) following temperate natural forest development in China. The objectives of this study were to examine the variation of soil aggregate associated OC decomposition rates, quantify the changes in the proportion of new and old soil aggregate OC, and explore the effects of controlling factors on SOC stocks, rate of total SOC increase and decomposition rate constants. The results showed that soil aggregate associated OC sequestration increased in 0−10 cm soil depth, while decreased in 10−30 cm soil depth. However, rate of aggregate associated OC increase, decomposition rate constants, and proportion of new OC increased at the early stage and then decreased along with the natural vegetation restoration. In addition, land use change had an important effect on soil aggregate associated OC dynamics, and soil particles, BD, MWD, C: N, plant diversity also played an important role. Moreover, SOC stocks had a negative relationship with clay and silt, while had a positive relationship with MWD and sandy soils. decomposition rate constants had a negative relationship with plant diversity, silt, and sand, while had a positive relationship with C: N and MWD. The proportions of new SOC had significant positive relationships with C: N, and it had a negative relationship with clay and silt. Therefore, it is necessary to clarify the formation mechanism of soil particles and aggregates, improve plant biodiversity, regulate the soil C: N ratio, and improve soil particle structure to increase soil carbon sequestration.