The work aims to solve the problems in the current stereo warehouse in the cold chain logistics industry such as high loss rate, serious temperature loss and low level of informatization, so as to ensure the food quality and safety in the cold chain intelligent stereo warehouse, and realize cost reduction and efficiency increase. Aiming at the operation scenario of cold chain intelligent stereo warehouse, a five-dimensional digital twin model with full mapping and multi-dimensional simulation was designed. Through the fusion of multi-source heterogeneous data, real-time visualization and monitoring and early warning of all elements in the stereo warehouse were realized, and a model optimization strategy that supported system linkage decision-making was proposed, which intelligently adjusted the load of the stereo warehouse and the thermal distribution in the temperature control area to maximize the operation efficiency and reduce operation costs. A set of digital twin system was constructed for the cold chain intelligent stereo warehouse. The comparison on the warehouse operation data before and after optimization, the food freshness loss rate decreased by 25%-30% year-on-year under the same storage environment conditions, and the accurate mapping and linkage operation of real-time data and dynamic virtual model of cold chain intelligent stereo warehouse was realized.Taking the cold chain stereo warehouse of Foshan Intelligent Cold Chain Warehousing and Logistics Center, a supply chain management company in Guangdong as the practice object, a new model of integrated management and control of cold chain intelligent stereo warehouse is formed, which provides an application reference of digital twin technology for cold chain intelligent stereo warehouse operation management, scheduling linkage decision-making and collaborative operation, and provides a new path for establishing a better fresh product packaging and ensuring cold chain food quality and safety.