How to achieve greater crop productivity with lower greenhouse gas (GHG) emissions from limited farmland has been a hotspot of interest in global agricultural production. In this study, we analyzed the effects of legume intercropping and nitrogen (N) fertilizer level on net greenhouse gas balances (NGHGB), yield-based greenhouse gas emissions intensity (GHGI), carbon footprint (CF) and crop productivity in sweet maize cropland in South China based on a long-term field experiment during 2013-2018. Results demonstrated that the sweet maize/soybean intercropping pattern could improve crop productivity on the unit of arable land, but the yield advantage of the intercropping system was totally derived from the soybean. Accordingly, the intercropping pattern reduced the GHGI with significant difference compared to the sweet maize mono-cropping system. Therein, the difference between the sweet maize/soybean intercropping with crop line ratios of 2:3 (S2B3) and 2:4 (S2B4) were not significant. Furthermore, suitable N input during the sweet maize cultivation in the region were necessary for improving the crop productivity and decreasing the GHGs emission in farmland. Also, the difference of N levels was significant to the GHGs emissions, soil organic carbon sequestration, GHGI and NGHGB. The 300 kg N ha(-1) showed the better effect for lowering the NGHGB and CF in sweet maize farmland when keeping crop productivity. The interaction effect of the N level and crop pattern just showed on the crop yields and GHGI. The S2B4 with 300 kg N ha(-1) showed significant benefits with respect to maintaining the yields and reducing the net GHGs emissions compared to conventional sweet maize farming system in the Pearl River Delta in China. These advanced agricultural practices contributed to the development of clean agricultural production in China.