Ecological supply chain is an improvement to traditional supply chain according to ecological thinking. There are four sub-systems in ecological supply chain, i.e. production system, consumption system, social system and environmental system. The formation of ecological supply chain is the interacting result of various factors, which not only include pressures from government, customer and other stakeholders, but the impetuses from firms and the system itself. The cooperation processing based on by-products exchange is discussed with the decision-making criterion of eco-efficiency maximization. Accordingly, a pricing model is given.