Soil carbon is crucial for soil fertility and plant growth in agricultural systems that were affected by reclamation from local natural soil and agricultural management measures. To explore the effects of reclamation and agricultural management measures on soil organic carbon (SOC) and microbial biomass carbon (MBC), a 37-year long-term positioning field experiment site in Shenyang Agricultural University of China was applied to investigate the distribution changes of SOC and MBC from topsoil (0-20cm) to subsoil (20-40cm) between local natural soil (LNS) and the cultivated soil with agricultural measures of mulching (F) and fertilization. The results showed, after reclamation, the SOC content in the topsoil in the CK treatment without mulching (NF) decreased by 23.35%. The SOC content in the subsoil with F and NF treatments after reclamation was higher than that in LNS by 19.44% and 12.41%. MBC showed a decreasing trend in the topsoil after cultivation, but significantly increased in the subsoil. F plus high amount pig manure (FM 4) treatment resulted in SOC accumulation in the topsoil approaching the level before reclamation and significantly enriched SOC in subsoil. Under NF conditions, combined application of medium organic and nitrogen fertilizers (M 2N 2) treatment increased MBC by 134.9%. Moreover, SOC and MBC showed a significant positive correlation in LNS, while agricultural measures reduced the corrlation, indicating a significant negative correlation in the subsoil by mulching ( P<0.001). Available potassium and available phosphorus positively regulated SOC accumulation ( P<0.05), while bulk density and the carbon and nitrogen ratio inhibited carbon sequestration in soil. Overall, reclamation and agricultural measures induced the distribution difference of SOC and MBC between top-and subsoil. The soil carbon in the subsoil after reclamation showed a stable growth trend by mulching and high amount organic fertilizer input, which suggested that it is vital to subsoil management on agricultural soil utilization.