Based on the DNDC model, the carbon storage of farmland ecosystem in Hailun City during 2010–2060 was simulated and predicted, and the interannual dynamics of soil carbon source/sink in the farmland ecosystem in Hailun City were analyzed. The results showed as follows: (1) The SOC content of soil simulated by DNDC model in 2017 was compared with the soil organic matter survey results of Hailun Agricultural and Rural Bureau in 2017. The root-mean square error is 0.009 kg·C/kg, and the average absolute percentage error is 28.49%. It can be seen that the DNDC model can simulate soil SOC content change in Hailun City well. (2) According to the simulation results, after excluding the years affected by bad weather, it was found that planting corn was conducive to SOC accumulation in the comparison of multiple planting systems. (3) If the soybean recropping system continues to be implemented, the surface SOC in the study area will remain in the state of carbon source, which is not conducive to the implementation of the national carbon peak strategy in 2030. (4) According to the simulation results, a reasonable arrangement to implement alternating planting systems of corn-soybean rotation and corn recropping during 2022–2060 can ensure that the typical black soil area of Hailun can reach the state of carbon sequestering in 2030 and in the future (2030–2060) for a long time, supporting the action plan of carbon peak and carbon neutrality. It has a good guiding effect on agricultural planting in the study area.