Increasing agricultural yields and reducing greenhouse gas (GHG) emissions are the main themes of agricultural development in the 21st century. This study investigated the yield and GHGs of a jujube–alfalfa intercropping crop, relying on a long-term field location experiment of intercropping in an arid region. The treatments included four planting densities (D1 (210 kg ha−1 sowing rate; six rows), D2 (280 kg ha−1 sowing rate; eight rows), D3 (350 kg ha−1 sowing rate; ten rows)) and four nitrogen levels (N0 (0 kg ha−1), N1 (80 kg ha−1), N2 (160 kg ha−1), and N3 (240 kg ha−1)) in the jujube–alfalfa intercropping system. The results showed that the jujube–alfalfa intercropping system is a the “source” of atmospheric CO2 and N2O, and the “sink” of CH4; the trend of CO2 fluxes was “single peak”, while the trend of N2O and CH4 fluxes was “double peak”, and there was a tendency for their “valley peaks” to become a “mirror” of each another. The magnitude of emissions under the nitrogen level was N3 > N2 > N1 > N0; the content of soil total nitrogen, quick-acting nitrogen, and the global warming potential (GWP) increased with an increase in the amount of nitrogen that was applied, but the pH showed the opposite tendency. The D2N2 treatment increased the total N, quick N, SOC, and SOM content to reduce the alfalfa GHG emission intensity (GHGI) by only 0.061 kg CO2-eq kg−1 compared to the other treatments. D2N2 showed a good balance between yield benefits and environmental benefits. The total D2N2 yield was the most prominent among all treatments, with a 47.64% increase in yield in 2022 compared to the D1N0 treatment. The results showed that the optimization of planting density and N fertilization reduction strategies could effectively improve economic efficiency and reduce net greenhouse gas emissions. In the jujube–alfalfa intercropping system, D2N2 (eight rows planted in one film 160 N = 160 kg ha−1) realized the optimal synergistic effect between planting density and nitrogen application, and the results of this study provide theoretical support for the reduction in GHGs emissions in northwest China without decreasing the yield of alfalfa forage.