Based on Stackelberg's master–slave game theory and green index decision-making conditions, this paper studies the benefit coordination of a supply chain network composed of a business flow network and logistics network, discusses the decision-making behavior of the main body of the supply chain network under the performance of green contracts or speculative behavior, respectively, and further constructs the supply chain network collaborative benefit coordination model under the guidance of a manufacturer considering a green development index. The supply chain network interest coordination model analyzes the relationship between the dominant manufacturer behavior and the supply chain network green index and network profit. The results show that fulfilling green contracts helps improve the profitability and sustainability of supply chain networks. A counter-intuitive but interesting result is that the dominant manufacturers increase the cost-sharing ratio or penalties of the logistics network, which will reduce the profit level and green index of the logistics network, and increase the cost-sharing ratio or punishment of the suppliers. Strength will increase the profitability and green index of the logistics network. Finally, we validate the relevant conclusions of the model through numerical simulation analysis.