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In NCS (networked control systems), the control performance depends on not only the control algorithm but also the communication protocol stack. This paper presents a framework for the protocol reconfiguration in NCSs. Task queuing, network transmission policy and communication link control are emphasized as three key protocol functionalities related to the system performance. Based on it, data and event exchange models for layers of protocol stack are developed according to the standard IEC61499, which allows for the dynamic reconfiguration management of distributed resources as well as provides a unified real time communication service for control tasks. Finally, experiments are conducted to illustrate the application and efficiency of the proposed reconfigurable protocol stack.