According to the theoretical and practical experiences of agricultural supply chain both at home and abroad and the principles of profitability, efficiency, sustainable development, closed-loop supply chain mode of ecological agriculture embedded with knowledge scheme is constructed based on the urban and rural two-way logistics system. This mode is embedded with technical knowledge program of eco-crop cultivation and management during the logistics distribution of agriculture means of production. Profit is obtained through the connection between eco-agricultural production base and market. Support system of this mode is introduced, including technology, policy, management, human resources and financial support. Stage characteristics and evolutionary process of closed-loop supply chain of ecological agriculture are analyzed from the periods of incubation, growth, maturity to recession. Applicability of the closed-loop supply chain mode of ecological agriculture embedded with knowledge scheme is discussed from the aspects of capital, logistics network channels, and human resources coordination. Taking Guangxi Kanghua Ecological Agriculture Plantation Development Co. Ltd, as an example, operation process of supply chain is summarized; and the practical significance and popularization value of closed-loop supply chain of ecological agriculture embedded with knowledge scheme are verified.