Today, consumers are increasingly demanding higher quality in fresh agricultural products. The issues that need to be addressed now are how to keep fresh products fresh and how to coordinate the operations of supply chain participants. Three decision models are developed in this paper using the Stackelberg model: supplier-led decision making, retailer-led decision making, and centralized decision making. The comparative model analysis shows the following: (1) Regardless of the decision model, the supply chain system under centralized decision-making is always more profitable than the supplier-led or retailer-led one. (2) The optimal profit and freshness preservation strategy of the supply chain system depends on the sensitivity coefficient of consumers to price and freshness. (3) Suppliers and retailers can coordinate the costs of freshness inputs according to how the cost-sharing coordination contract is structured. (4) Finally, the numerical analysis is applied to demonstrate the correction of the model.