This paper discusses the supply chain optimization problem in the event of happening of unexpected circumstances and the relevant data about the actual system state (delivery status, preserving temperature, actual stock, availability of transport facilities, etc.) could be timely obtained. To optimize the receiving process of current information, the scheduling problem of retrieving and handling the information is considered. To describe supply chains operation and optimize it, we use the dynamic systems with control and design optimal program and position controls. The advance of this paper is that cyber-physical system has been applied in the SC optimization problem when it is essential to do real-time reaction when unexpected circumstances happen for improving the timeliness of the relevant data about the actual supply chain state. We combine the considered models and apply the classical control theory methods to solve this supply chain management problem.