Soil organic carbon (SOC) plays a crucial role as a nutrient trigger and directly impacts soil health and agricultural productivity. In China, the Well-facilitated Farmland Construction (WFC) Project is a comprehensive agricultural management strategy, changing the soil environment and then influencing the SOC dynamics. However, the long-term trajectory of SOC under the implementation of the WFC Project remains unclear. To address this knowledge gap, this study focused on farmland in southeastern China that completed the WFC Project in 2022. A total of 202 topsoil samples (0–20 cm) were collected from the regional paddy soil in 2023. Using digital soil mapping (DSM) and the CENTURY model, we delineated key soil properties and simulated the spatio-temporal changes of SOC density (SOCD). The results revealed that the SOCD ranged from 1.23 to 6.35 kg m^–2, with an average value of 3.68 kg m^–2 in 2023. Soil pH, clay, and sand content were primary factors influencing SOCD distribution. According to CENTURY model simulations, SOCD exhibited a declining trend from 2010 to 2021, while it was projected to increase from 2022 to 2030 following the WFC implementation, which could be attributed to enhancements in irrigation and straw incorporation. Besides, the scenario without WFC results shows that SOCD would decline from 2022 to 2030, underscoring the project’s effectiveness in preventing SOC loss for paddy soil. The spatial patterns of SOCD in 2021 and 2030 were similar, and the low-value areas showed faster increase rates than the areas with high SOCD levels, indicating that the specific field plots with lower SOCD levels could sequester more carbon with improved soil management. In conclusion, the WFC Project can potentially increase SOC sequestration in the paddy soil and grain yield, ensuring food security and addressing climate change.