Today, the DeNitrification DeComposition (DNDC) is model used to anticipate soil organic carbon (SOC) turnover and crop growth under various field management practices. Gorgan County is an important region for soybean production in Iran. We aimed to 1) validate the DNDC model for modeling SOC dynamic in croplands under soybean cropping, 2) simulate the total topsoil (0–30 cm) SOC stocks of soybean cropping systems, 3) quantify the spatial distributions of carbon sequestration potential of soybean-grown croplands by Geographic Information System (GIS) techniques. In this research, soil samples were taken from 150 fields at depth of 0–30 cm before soybean cultivation and after crop harvesting. In this research, we used the site simulation type of DNDC model for simulation and denitrification/decomposition procedure. Inputs in the DNDC model included information on survey region, climate, soil, crop properties, and farmland management practices. The soil and crop properties categorized into farming management practices such as fertilization, tillage, grazing or plant cutting, and irrigation. The climatic data were obtained from one meteorological station located within the study area. To continue, crop parameters were provided based on field survey and laboratory work. Also, the soil properties (including texture, bulk density, pH, SOC, soil total N, field capacity, wilting point, hydro-conductivity point, porosity and clay fraction) were obtained from sampling sites distributed in soybean croplands of Gorgan county. Results indicated that the DNDC model can simulate the SOC values for soybean fields. Based on the results, there was correlation between the simulated and measured data for SOC. The average concentration and storage of carbon sequestration were as 3.97 and 1.42 Mg ha-1 for observed situation and in predicted situations obtained as 2.60, and 1.42 Mg ha-1, respectively. The highest content of SOC was related to the east, southeast, and central parts toward the south of the county, which was affected by several factors such as soil bulk density, regional climatic condition, using conservation cropping systems, improved irrigation systems, and fertilization management type. The study provided new information on how improvements in the process-based DNDC model in Iran. Therefore, it can be utilized to determine SOC change and dynamism and carbon sequestration potential on the regional scale.