Soil aggregates are important carriers of soil organic carbon (SOC) accumulation, and play an important role in the evaluation of soil structure and quality. Natural recovery can promote change in soil aggregate structure and quantity via the redistribution of SOC in the aggregates. Natural restoration from farmland is an important vegetation restoration model on the Loess Plateau. The changes in soil aggregate structure and soil carbon stock after natural restoration have received extensive attention. However, little is known about the continuous study of soil changes on the abandoned grassland during the recovery process. Therefore, to understand how SOC accumulates in the process of natural recovery and quantitatively analyze the contribution of aggregates to the total soil carbon pool, we selected four abandoned grasslands of different restoration ages on the Loess Plateau, China, and studied the changes in soil structure, soil total organic carbon (TOC), soil C:N, soil aggregate distribution, soil aggregate stable index (mean weight diameter, MWD; geometric mean diameter, GMD), and aggregate-associated SOC changes as well as their correlations from 0-20 cm and 20-40 cm soil layers in abandoned grasslands. In addition, we calculated the contribution of aggregates with different sizes to soil TOC stock. The results showed that:① natural restoration increased the macroaggregate amount, MWD, and GMD, but decreased the amount of microaggregate and silt-and clay-sized fractions. There are significant differences in the distribution and stability of aggregates between different soil layers; the promotion effect of the surface was higher than that of the subsurface soils. ② In the 42 years after abandoning recovery, soil TOC stock, macaggregate-and mesaggregate-associated SOC stock increased significantly, and varied with soil depth and years of abandonment (1.92 times, 10.2 times, and 3.61 times). In contrast, micaggregate-associated SOC stock decreased significantly, and silt-and clay-sized fractions-associated SOC stock showed no distinct change. In addition, natural restoration promoted the ratio of C:N; nevertheless, the ratio of C:N under the surface showed a reduced phenomenon after 42 years of abandonment. ③ The improvement in soil TOC stock depends primarily on changes in the macaggregate-associated organic carbon stocks, which account for 80% of macaggregate, and the significant increase in the amount of macaggregate is the main reason for the high contribution.The results of our study suggest that natural restoration is conducive to the accumulation of soil organic carbon, and improvement in soil structure and stability. Macroaggregate is the key factor in soil organic carbon accumulation and soil structure improvement in the process of natural restoration.