Changes in soil organic carbon (SOC) of rice paddies in China were simulated from 1980 to 2000 by linking a coupled bio-physical model to GIS database. The coupled model consists of two sub-models including Crop-C for simulating net primary productivity and hence residue retention and Soil-C for computing the turnover rates of SOC. The GIS database included parameters of climate, soils and agricultural activities with the resolution of 10 km × 10 km. Model simulation indicated that Chinese rice paddies covering 22.6 Mha sequestrated a considerable amount of C, about 0.15 ± 0.07 Pg C from 1980 to 2000. Annual sequestration rate increased sharply from -180 ± 45 kg C ha-1 year-1 in 1980 to 440 ± 170kg C ha-1 year-1 in 1989. Thereafter, a steady sequestration rate of 460 ± 170 kg C ha-1 year-1 occurred till 1994 and declined since then. Approximately 84% of the Chinese rice paddies sequestrated carbon, while 15% lost carbon and 1%kept balance over the 20 years. Great SOC sequestration occurred in eastern, southern and central China, while a slight decline of SOC existed in some regions of northeastern and southwestern China.