The greenhouse gases such as methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2) were increased in atmospheric concentration since 1750, which attracted more and more attention regarding climate change. Agriculture activities contributed to the increase of greenhouse gas concentration in the atmosphere, resulting in high global warming potential, which was estimated to contribute about 47%~58% of the total anthropogenic emissions of CH4 and N2O. Film mulching is reported to be a significant agricultural factor which greatly affected greenhouse gas (GHG) emissions and the carbon footprint. The annual GHG emissions (CO2, CH4 and N2O) from a wheat-maize rotation system during 2014—2015 were monitored by using the static opaque chamber and gas chromatography technique in Guanzhong Plain of China. Four mulching treatments were no mulching (CK), semi-film mulching (BM), ridge-furrow planting with film mulching over ridge (LM) and whole film mulching (QM). Net global warming potential (NGWP) and carbon footprint were used to evaluate the effect of film mulching on GHG emissions and composition of carbon footprint production. The results showed that compared with CK, the BM, LM and QM treatments increased annual crop yield by 9.0%, 16.5% and 26.6%, respectively. Similarly, the BM, LM and QM treatments increased annual CO2 emission by 33.9%, 9.3% and 31.6% and annual N2O emission by 22.9%, 14.3% and 47.1%, respectively. However, annual CH4 emissions showed no significant difference compared with CK. In addition, NGWP was increased by 9.0%, 16.7% and 26.0%, respectively. The carbon footprint of LM and QM treatments was 33.2% and 21.9% lower than that of CK, while BM treatment showed no significant difference compared with CK. Compared with carbon footprint per unit crop yield of CK, that of BM treatment was increased by 16.3%, while that of LM treatment was decreased by 13.1%. Meanwhile, QM treatment showed no significant difference. Considering both the economic and environmental effects of different mulching treatments, ridge-furrow planting with film mulching over ridge in the wheat-maize rotation system was recommended for carbon sequestration and greenhouse gas reduction in Guanzhong Plain of China with the purposes of water saving and carbon sequestration.