Strict control taken in response to public health emergencies (PHEs) can hinder fresh products supply, while stock-outs and the risk of epidemics can increase fresh products demand. To explore the interrelationship between outbreak control measures and the availability of fresh products, this paper establishes a dynamic synergistic model of epidemic transmission subsystem and fresh products supply-consumption subsystem based on system dynamics (SD). Taking the spread of COVID-19 in Shanghai from March to May 2022 as the actual background, the impact of different storage strategies and control measures on epidemic prevention and material supply was quantitatively evaluated. The results show that risk transmission factor (RTF) affects the number of infections and the intensity of community control contributes to controlling the spread of the epidemic, but it can continue to affect fresh product supply security. Therefore, increasing fresh product protection inputs and reducing in-transit time can reduce fresh product losses and improve fresh product supply security under PHEs. The findings can enable fresh products to effectively match supply and demand under PHEs, mitigate the impact of epidemic risks and provide decision support for relevant retailers.