From the perspective of deepening the structural reform of the supply side of rural finance, and with respect to the basic characteristics of the new agricultural operation system, we innovatively apply the basic principle of supply chain finance to a new agricultural operation system, and develop specific types, links, and modes of application. We also use the dual Stackelberg game model to build a revenue function for new agricultural operation entities and financial institutions, and use the reverse solution method to determine the conditions for both the optimum production of agricultural product suppliers and the optimal loan rates of financial institutions, making the decision-making mechanism of supply chain finance more realistically applicable in the new agricultural operation system. Based on the above, we propose specific solutions such as highlighting risk management, improving operation conditions, and others to ensure the innovative application of supply chain finance in the new agricultural operation system.