Organic carbon dynamics of intensive agricultural soils is significant for sustainable crop production. Huang-Huai-Hai plain is the most important region for grain production with wheat-corn rotation as its main cropping system in China. In this region, the soil texture is restricted in the range between sandy loams and loamy clays, the variation in pH to values mostly between 7.38 and 8.55. CQESTR is a model to estimate carbon sequestration in agricultural soils. With the calibration of parameters by short- and mid-term buried organic material experiments, the CQESTR model was modified according to four stages of biomass decomposition; at different stages the biomass factors were determined. Through the validation of soil organic matter (SOM) by 7 independent long-term experiments of soil fertility and fertilizer efficiency in this region, the modified CQESTR model can predict the mineralization of residue, added organic amendment and native SOM based on cropping practices, thus predicting the effect of tillage and crop rotation on organic carbon decomposition and storage in agricultural soils. The modified model provides estimates with a 95% confidence interval of 1.91 g kg-1 and regression coefficient r2 of 0.91 on 1151 pairs of fitted and observed SOM in the plough layer. The modified model performs better than the original one.