The rapid specialization of livestock production in China has contributed to spatially decoupled crop and livestock production, leading to various environmental pollution issues. Some regional agro-environmental policies have recently promoted the coupling of specialized crop and livestock farms through cooperation. However, the environmental and economic performances of such cooperation remain unclear. This study investigated multiple environmental footprints of two contrasting production systems: cooperative crop-livestock systems (CCLS) and decoupled specialized livestock systems (DSLS), using survey data of 87 ruminant farms in Northwest China. Results show that farms in CCLS had lower net greenhouse gas (GHG) emissions (12–29%), lower reactive nitrogen (Nr) emissions (21–40%), lower phosphorus footprints (PF) (41–54%), and used less cropland (24–31%) per kg animal product, compared to those in DSLS. The large differences in GHG emissions between the two systems were mainly related to enteric fermentation and resource production (used for feed production). The differences in Nr emissions and PF were mainly related to manure management. Net profits per kg animal product were higher in CCLS (13–35%) than in DSLS, and most profits originated from lower purchasing costs of feed and young livestock. Net profits and environmental footprints were negatively correlated, suggesting an environmental and economic win-win situation for CCLS. The possible obstacles to recoupling specialized crop and livestock farms through cooperation have been discussed, including farm size, contract stability, and local policies. Our study provides science-based evidence to support policymakers and specialized farms to close nutrient loops between crop and livestock production sectors through regional cooperation.