In view of the three-level supply chain consisting of single fresh supplier, fresh e-commerce and third-party logistics, a research has thus been conducted on the pricing and coordination issues of the fresh agricultural product supply chain, taking into consideration the impact of price and freshness on the demand for fresh agricultural products. First of all, the pricing models are constructed of fresh agricultural products supply chain under centralized decision-making and decentralized decision-making dominated by fresh suppliers, followed by a comparative analysis. Secondly, on the basis of a decentralized decision-making, a coordination model is constructed by using a “revenue sharing plus fresh-keeping cost sharing” contract construction coordination model. Finally, the conclusions drawn by the model can be verified through a case analysis and sensitivity analysis, followed by an analysis of the impact of important parameters on the model. It is found that retail prices, preservation efforts, and supply chain profits under centralized pricing decisions are superior to the corresponding values of decentralized pricing decisions. Based on this, it is recommended to adopt a “profit sharing plus preservation cost sharing”contract coordination model, which helps to achieve a coordinated state in the supply chain under decentralized pricing decisions.