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The protocol stack plays a critical role in determining the performance of Networked Control System (NCS), which governs the communication activities and directly affects the communication Quality of Service (QoS). Full or partial reconfiguration of protocol stack offers both optimized communication service and system performance. This paper proposes a formal approach for the design and implementation of reconfiguration protocol stack based on Specification Description Language (SDL) for NCS. In Telelogic TAU environment, detail SDL models to support communication and reconfiguration functions of communication link layer, network transmission layer and application layer are discussed respectively. The MSC verification results validate the effective of our reconfiguration concepts on the protocol implementation for NCS.