In the context of government restrictions on carbon emissions of enterprises, the optimal decisions such as preservation effort level and packaging recycling price in the three-level supply chain of e-commerce platform-supplier -TPLSP were studied on fresh food products that are easily corrodible and difficult to store. The decision-making and system benefits of fresh food supply chain were compared and analyzed with TPLSP adopting packaging recycling strategy or without under decentralized decision-making. The effects of carbon trading price, freshness degree and recycling price preference degree on supply chain system profits and emission reduction effects were analyzed based on the centralized mode of supply chain system with higher efficiency to construct an optimized contract combining quantity discounts and two-part fees. The results show that the carbon trading price is positively correlated with the packaging return rate of consumers, while it does not increase the market demand for fresh products. When consumers’ preference of freshness and price sensitivity of fresh food packaging recycling are high, the supply chain system has higher economic benefits. When the parameters are within a reasonable range, the coordination and optimization of supply chain system can be realized through quantity discount and two-part fee combination contract.