This study examines the Dalian Tieyue Cold-Chain Logistics Center and, using the FlexSim platform, develops a cold-chain operations simulation model calibrated with actual loss data. The model jointly considers material flow, labor efficiency, equipment operating states, and fluctuations in the warehousing environment. By fitting to real operational records, it enables dynamic simulation and performance analysis of inbound, outbound, and material-handling processes. The results indicate that inbound operations are the primary source of losses, with equipment waiting and imbalanced workforce scheduling being key limiting factors. On this basis, three categories of measures are proposed—process optimization, improvements to workforce scheduling, and adjustments to warehouse layout—which, when validated via re-simulation, reduce the loss rate by approximately 12%