Aiming at the secondary supply chain system consisting of a single fresh E-commerce and a single agricultural product supplier，the Stackelberg Game model is used to solve the optimal strategy and maximum profit of suppliers under three different decision modes： centralized decision-making，fresh e-commerce-oriented decision-making and fresh agricultural product supplier-oriented decision-making. It is concluded that different dominant modes have different effects on the optimal strategy of supply chain. Different dominant modes also have different effects on the profits of supply chain enterprises. The maximum profits tend to be dominant，but the total profits of the two modes under decentralized decision-making are lower than those under centralized decision-making. Under the same dominant power，the profits of fresh E-commerce and suppliers will be different，and the profit of the dominant supply chain side will be greater.