Optimizing Irrigation and Nitrogen Inputs for Balancing Greenhouse Gas Mitigation, Productivity, and Profitability in an Intercropping System of Wolfberry and Alfalfa

Water and nitrogen management influences farmland productivity and greenhouse gas emissions by regulating the soil micro-environment. However, the synergistic optimization strategy among yield improvement, economic benefit, and emission reduction in intercropping systems in arid regions remains unclear. Based on a two-year field experiment using an intercropping system of wolfberry and alfalfa, this study established four irrigation levels [full irrigation (W0), mild water deficit (W1), moderate water deficit (W2), and severe water deficit (W3)] and four nitrogen application levels [0 (N0), 150 (N1), 300 (N2), and 450 kg·ha−1 (N3)]. The effects of water and nitrogen regulation on soil hydrothermal conditions, greenhouse gas emissions, crop yield, and economic benefits were systematically analyzed. The results showed that soil water content increased with higher nitrogen application rates but decreased with a more severe water deficit. In contrast, soil temperature exhibited the opposite trend, with the W3 treatment increasing by 2.23–2.41 °C compared to W0 during the full fruiting period. The emission fluxes of CO2 and N2O increased with higher nitrogen application rates but decreased with a more severe water deficit. CH4 acted as a sink, with its uptake decreasing as nitrogen application increased and the water deficit intensified. CO2 was the dominant contributor to the global warming potential of the intercropping system of wolfberry and alfalfa, accounting for 85.3–94.6% of the total. The emission fluxes of CO2 and N2O were significantly positively correlated with the soil water content, while the CH4 emission flux was significantly positively correlated with the soil temperature. The W0N2 treatment achieved the highest system yield and net profit, whereas the W1N2 treatment exhibited the highest return on investment. A comprehensive evaluation using the entropy weight–TOPSIS model identified W1N2 as the optimal treatment. An integrated water–nitrogen decision model determined that the optimal water and nitrogen combination for achieving a high yield, a high efficiency, and low emissions was an irrigation amount of 4245–4413 m3·ha−1 and a nitrogen application rate of 290–323 kg·ha−1. The findings of this study can provide a scientific basis for the sustainable water and nitrogen management of characteristic cash crop intercropping systems in arid regions.