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.