Agricultural management practices that increase carbon (C) sequestration and reduce greenhouse gas (GHG) emissions have been identified as attractive mitigation strategies. In this study, we evaluated the spatial-temporal dynamics of carbon footprints (CFs) in China and their driving factors aimed to analyze potential mitigation strategies. Our CF data comprised the GHG emissions and C sequestration of main crop production. The results indicated that from 2000 to 2015, the GHG emissions of main crop production reached 133.3 Tg CO-C equivalents (Ce) year and the soil C sequestration was 25.3 Tg Ce year, resulting in a CF of 108.0 Tg Ce year. In addition, the CF increased by only 1.9%, and 90.9% of the increase in GHG emissions was offset by C sequestration from straw return and fertilization. Moreover, the farm CF (FCF) and product CF (PCF) decreased by 9.7% and 30.4%, respectively, because the proportion of cropland practicing straw return increased by 26.4% and the improved efficiency of fertilization resulting from decrease in fertilizer use of 8 kg nitrogen (N) ha year. At the regional scale, GHG emissions increased by 9.1-65.0%, and the primary drivers underlying this change were fertilization, machinery operation and rice paddy CH flux in the northeast-northwest, north and south, respectively. However, the PCF decreased by 15.0-47.0% as soil C sequestration increased because of the decreased use of fertilizer and the implementation of straw return. The expansion of straw return and promotion of fertilization efficiency significantly mitigated 25.3 Tg Ce year emissions, indicating that these measures are important mitigation strategies and should be implemented specifically in different regions combined with other management practices. Our study provided a comprehensive method of calculating the CF of croplands and its driving factors in China and indicated potential mitigation strategies that would benefit policy selection for reduced emissions without influencing crop yields.