Abstract: Both the factory production of greenhouse vegetables and the E-commerce are in a stage of vigorous development in China, but are confronted with enormous challenges in deeper integration. Improving the value stream of greenhouse vegetable production, and integrating the supply chain of fresh vegetables and agricultural products of greenhouse, could provide new opportunities for the development of modern greenhouse agriculture. In view of the existing problems in E- commerce supply chain of greenhouse vegetables, countermeasures are put forward. The types, characteristics, and influence factors of greenhouse ecological economic system are discussed. This research also proposes a way to improve the value stream of the greenhouse ecological economic system of E-commerce supply chain, and provides references for innovating the circulation mode of greenhouse fresh vegetables, accelerating transformation and upgrading of greenhouse vegetable market system.