Life cycle assessments (LCA) of staple food (rice, wheat and corn) production and assessments of the associated greenhouse gas (GHG) and reactive nitrogen (Nr) releases from environmental and ecological perspectives help to develop effective mitigation options. Therefore, carbon (C) and nitrogen (N) footprint reductions in agroecosystems have become an increasingly popular topic related to global climate change and agricultural adaptation. The LCA method was used to calculate the product and farm C footprint (CF) and N footprint (NF) of double rice, rice-wheat and wheat-maize production based on governmental statistical datasets and published results. The spatial and temporal patterns of CF and NF were analyzed in China during 2004–2017, and their driving factors were analyzed to identify potential mitigation strategies. The results showed that of the various inputs, fertilizer application and diesel oil consumption contributed the most to both GHG and Nr emissions from farm inputs in the grain crop production process. The CFs for double rice, rice-wheat and wheat-maize were 0.83, 0.74, and 0.37 kg CO2-eq kg−1 year−1 at the yield scale, respectively. In addition, the NFs were 11.6, 13.4, and 15.4 gN-eq kg−1 year−1 at the yield scale for double rice, rice-wheat and wheat-maize, respectively. The largest fraction of CF and NF was the share of CH4 emissions and NH3 volatilization from the field soil, respectively. The annual CFs and NFs of the multiple crop in the southwestern provinces were higher than those in the central and northern provinces. The annual GHG and Nr emissions from the multiple crop maintained a relatively stable state from 2004 to 2017. The proportion of CO2/Nr production was partly reflected a soil C/N ratio, suggesting a higher C abundance for the double rice production, which could be used as a reference parameter for crop structure adjustment in the future. Based on our results and other studies, some effective solutions, especially optimized fertilization, farm machinery operation efficiencies and changes in regional allocation of grain cropping areas, are needed to mitigate the impacts of climate change and eutrophication on the main grain crop production in China.