Much concern has been raised about how multifactor global change has affected food security and carbon sequestration capacity in China. By using a process-based ecosystem model, the Dynamic Land Ecosystem Model (DLEM), in conjunction with the newly developed driving information on multiple environmental factors (climate, atmospheric CO2, tropospheric ozone, nitrogen deposition, and land cover/land use change), we quantified spatial and temporal patterns of net primary production (NPP) and soil organic carbon storage (SOC) across China's croplands during 1980–2005 and investigated the underlying mechanisms. Simulated results showed that both crop NPP and SOC increased from 1980 to 2005, and the highest annual NPP occurred in the Southeast (SE) region (0.32 Pg C yr−1, 35.4% of the total NPP) whereas the largest annual SOC (2.29 Pg C yr−1, 35.4% of the total SOC) was found in the Northeast (NE) region. Land management practices, particularly nitrogen fertilizer application, appear to be the most important factor in stimulating increase in NPP and SOC. However, tropospheric ozone pollution and climate change led to NPP reduction and SOC loss. Our results suggest that China's crop productivity and soil carbon storage could be enhanced through minimizing tropospheric ozone pollution and improving nitrogen fertilizer use efficiency.