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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 finite state machines (FSMs) approach for modeling analysis of reconfiguration protocols stack in NCS. The proposed reconfiguration architecture is implemented by illustrating a simulation for the flexible scheduling scheme on the Ethernet protocol. Detail FSM implement modules for composing node models of master and salve are discussed respectively in OPNET environment. The simulation results validate the effective of our architectural concepts on the protocol implementation in NCS.