Optimising Nitrogen Fertiliser Management in a Goji Berry–Alfalfa Intercropping System for Dual Benefits of Emissions Reduction and Yield Enhancement in Arid Regions

Background: Amidst the pressing need to balance global food security and climate governance, achieving synergistic optimisation between crop yield enhancement and agricultural greenhouse gas reduction has become the central imperative for advancing the transition to green agriculture. Purpose: To investigate the effects of cropping systems and nitrogen fertiliser application on goji berry production systems in arid regions. Method: This study employed two cropping systems (goji berry–alfalfa intercropping (I), goji berry monocropping (M)), and four nitrogen application rates (N0 (0 kg ha−1), N1 (150 kg ha−1), N2 (300 kg ha−1), N3 (450 kg ha−1)). The effects of planting patterns and nitrogen fertiliser regulation on the physicochemical properties of goji berry farmland soil, greenhouse gas emissions, and yield were analysed. Result: (1) Soil temperatures under I were significantly lower than under M, and nitrogen application levels, cropping systems, and the interaction between nitrogen application and cropping systems significantly influenced soil nutrients; (2) Cultivation patterns and nitrogen application levels exerted a highly significant influence on soil greenhouse gas emission fluxes in goji berry fields. CO2 emission flux peaked under IN3 treatment (annual average: 342.45 mg m−2 h−1), while N2O emissions peaked under MN3 (annual average 0.23 mg m−2 h−1). CH4 absorption was highest under MN0 (annual average −0.25 mg m−2 h−1); (3) Cropping systems and nitrogen application rates significantly influence greenhouse gas indicators including cumulative CO2 emissions, cumulative N2O emissions, and GWP. At the same nitrogen application level, GWP decreased by 5.63% on average in M compared to I, while under the same cropping system, N3 increased by 62.45% on average in N3 compared to N0; (4) Cropping systems and nitrogen application levels significantly influenced goji berry yield and economic returns. Under the same cropping system, N2 yielded the highest goji berry production and return on investment, with I and M yielding 2768.99 kg ha−1 and 4.06 and 3067.78 kg ha−1 and 3.15, respectively. Conclusions: The IN2 reduced soil greenhouse gas emission fluxes, cumulative emissions, and global warming potential while simultaneously increasing goji berry yield, net revenue, and return on investment. This approach minimises land resource wastage and represents a management model for achieving high yields with reduced emissions in goji berry fields within the Yellow River diversion irrigation districts of Gansu Province and similar ecological zones.