It is the goal of agricultural development to achieve the comprehensive benefits of high yield, high water and nitrogen efficiency but low environmental damage. However, the comprehensive benefits of greenhouse gas (GHG) emissions, grain yield, water and fertilizer efficiency in fertilized fields with different film mulching irrigation remain unclear. Therefore, we conducted typical maize field observation experiments based on drip irrigation under mulch (DM) and border irrigation under mulch (BM) for three years to quantify GHG emissions and their influencing factors, and analyzed maize yield, irrigation water use efficiency (IWUE), partial factor productivity of applied nitrogen (PFPN) and greenhouse gas emission intensity (GHGI). In our experiment, NO emissions were lower by 32.46%, CH absorption was higher by 23.49%, and CO emissions were lower by 4.53% under DM than under BM. The roles of different environmental factors in controlling GHG fluxes were different under two treatments. The relative importance of soil NO−N content to NO and CH fluxes under DM was the greatest, and the values were 0.61 and 0.47, respectively. The soil NH−N content had the greatest relative importance to CO flux under DM (0.43), CH flux under BM (0.72), and CO flux under BM (0.52). In addition, the maize yield, IWUE and PFPN under DM were 17.85%, 17.90% and 71.84% higher than those under BM, while the global warming potential (GWP) and GHGI under DM were 6.65% and 20.79% lower than those under BM, respectively. Our research provides a more comprehensive understanding of typical farmland management practices in arid areas and has important implications for agricultural development.