China is the world’s largest apple producer, and agricultural cooperatives play an important role in promoting sustainable production in its whole life cycle system. However, few studies on cooperatives have evaluated the environmental and economic performance from the life cycle thinking perspective. In this study, the combined methods of life cycle assessment (LCA) and life cycle cost (LCC) were used to comparatively analyze the environmental and economic performance of apple production between cooperatives and smallholder farmers. The results showed that, compared to the smallholder farmers, cooperatives significantly reduced resource depletion and environmental impacts by 12.50–22.16% in each category. The total environmental index for the cooperatives was 7.44% and 22.09% lower than smallholder farmers; meanwhile, the total LCC was 2659.71 Chinese Yuan (CNY), 19.27% lower than smallholder farmers. However, the net profit was 2990.29 CNY for the cooperatives, 21.23% higher than smallholder farmers. The results indicated that cooperatives exhibited a higher net profit while having lower resource input, environmental impact, and LCC than smallholder farmers. Moreover, pesticides and fertilizers were identified as the most critical environmental hotspots. Moreover, human labor cost was the most significant contributor to the total economic cost of the apple production system. These findings provide insights into optimizing farm inputs for apple production and active participation in agricultural cooperatives to alleviate multiple environmental impacts while maintaining apple yield and improving economic benefits, intending to make a marginal contribution to promoting sustainable development of the apple industry in China.