The supermarket refrigeration system typically has a distributed control structure, which simple and flexible, however, neglects interactions between its subsystems. Practice shows that these interactions lead to a synchronous operation of the display cases. It causes excessive wear on the compressors and increased energy consumption. The paper focuses on the synchronization analysis and de-synchronization control. The supermarket refrigeration system is modeled as a piecewise-affine switched system. The system behavior is decomposed such that synchronization analysis can be completed by using the Poincare map. A new de-synchronization scheme is proposed, which includes two steps: the synchronization monitoring and the de-synchronization control. Thus, the early warning of the synchronization can be given and then the de-synchronization controller can be activated. The scheme achieves better control performance and can deal with the large scale refrigeration system with different system parameters in the display cases.