Apple production provides smallholders with low economic benefits, while high environmental emissions limit the sustainability of the apple supply chain. Furthermore, coordination to achieve greater economic benefits and environmental protection, thereby improving the sustainability of the apple supply chain, remains underdeveloped. Here, we have analyzed the current status of the economic benefits and environmental emissions of the apple production process and explored the level of collaboration within the apple supply chain, based on an analysis of farmer horticultural practices for high production, high economic benefit, and low environmental emissions, in combination with substance flow analysis. Our study showed that compared with traditional practice, high-yielding, high-efficiency practice allowed fruit yield, partial productivity of nitrogen fertilizer, and economic benefit to increase by 33%, 61% and 49%, respectively, while soil nitrogen residue levels decreased by 13%. The improvement and adoption of technology in the apple-planting process significantly improved the sustainability of the apple supply chain: the economic benefit increased by 63%, while the nitrogen footprint decreased by approximately 68%. Additionally, the application of integrated nutrient management technology in the apple planting process significantly improved the sustainability of apple production, thereby synergistically improving the economic and environmental impact of the apple supply chain.