Simulation models are being regarded as an important tool to simulate crop growth, soil nutrient dynamics and soil carbon sequestration and fast use of the embedded knowledge of crop-soil processes. The Decision Support Systems for Agrotechnology Transfer (DSSAT) model was used to simulate long-term continuous maize growth from 1990 to 2007 in Gongzhuling, Northeast China. Three levels of N treatments were simulated, including: (1) no N (N0), (2) 165 kg N ha(-1) from synthetic fertilizer (N165) and (3) 50 kg N ha(-1) from synthetic fertilizer plus 115 kg N ha(-1) from farmyard manure (N165M). Both measured and simulated results showed that the maize yield was significantly lower in the N0 treatment. The measured maize yield was higher in N165M than N165 treatments after 2003. The maize yield was also affected by the weather, especially during drought years. The simulated soil organic C (SOC) content was in good agreement with the measured data in the 0-30 cm depth for all treatments. The SOC density in the 0-30 cm depth decreased by 4,393 kg C ha(-1) (18 %) in the N0 treatment and 4,186 kg C ha(-1) (17 %) in the N165 treatment, while it increased by 13,628 kg C ha(-1) (54 %) in the N165M treatment during 1990-2007, indicating that the combination of inorganic fertilizer and organic manure improved soil quality after 27 years of organic amendment from 1980. Soil mineral N levels were significantly higher in the N165 treatment just before planting (averaged 289 kg N ha(-1)), associated with more soil N leaching during the growing seasons (24-155 kg N ha(-1)) in some wet years, while soil mineral N levels were much lower in both the N0 (averaged 52 kg N ha(-1)) and N165M treatments (averaged 54 kg N ha(-1)) associated with less N leaching (< 10 kg N ha(-1)) compared with the N165 treatment. This indicated that the use of farmyard manure increased the soil organic matter and immobilized mineral N. The model results further indicated that complete crop residue removal from the field after harvest was a main reason for the decline of the SOC in the N165 treatment, suggesting that crop residue should be left on the soil to maintain the SOC balance and promote sustainable agriculture. Thus, we conclude that the DSSAT CENTURY-based module is a useful tool to simulate soil nitrogen dynamics and predict soil organic carbon sequestration in long-term field conditions.