Cotton-winter fallow is the major cropping system of cotton in the Yellow River basin of China, which not only leads to a considerable waste of land and natural resources, but also high greenhouse emissions and a loss of reactive nitrogen. Replacing winter bare fallow in cotton production with February orchid as a cover crop is a new cropping system in this area, but its sustainability is still unknown. Therefore, a field experiment was conducted with two cropping systems (cotton-winter fallow and cotton-February orchid) under four nitrogen application rates (0, 112.5, 168.75, and 225 kg N ha⁻¹). Field observations were incorporated into a life cycle assessment to estimate the carbon footprint, nitrogen footprint, net ecosystem economic benefits, and economic benefits. The estimated carbon footprint per unit of sown area was 43.6–76.1% lower in the cotton-February orchid system than in the cotton-winter fallow system, mainly because of the increase in soil organic carbon. The cotton-February orchid system significantly increased the nitrogen footprint per unit of sown area by 6.7–11.5% under different application rates mainly because of the increase in N₂O emissions. The nitrogen application rate significantly impacted the carbon and nitrogen footprints. After accounting for changes in the nitrogen and carbon footprints, the cotton-February orchid system with 168.75 kg N ha⁻¹, which resulted in the highest net ecosystem economic benefits and economic benefits, resulted in a 25.0% reduction in nitrogen fertilizer applied and a 9.5% increase in net ecosystem economic benefits compared with the conventional cotton-winter fallow system and nitrogen fertilizer application rate (225.75 kg N ha⁻¹). Thus, adopting an integrated strategy combining February orchid as a cover crop and a reduced nitrogen fertilizer application contributes to improvements in green and sustainable cotton production systems in the Yellow River basin and other regions with similar ecological conditions.