Based on the agricultural products supply chain pattern of “agricultural cooperatives + processors + retailers”, the paper proposes the concept of “cooperative-led agricultural supply chain” for the first time. By the Stackelberg game theory, Shapley value and modified Shapley value, the paper analyzes the profit allocation for each subject in the alliance. Furthermore, the paper introduces empirical values and proposes reasonable profit allocation of each subject in the alliance. The results show that by modified Shapley value method the agricultural cooperative gets more profit than the basic profit allocation, while the processor and retailer get less profit, but the relationship among the alliance is still stable because the principal of allocation depending on contribution is applied. Based on the analysis above, reasonable profit-sharing contract can be designed by modified Shapley value to maintain stable agricultural products supply chain alliance.