In networked control systems (NCS), the control performance depends on not only the control algorithm but also the communication protocol stack. The performance degradation introduced by the heterogeneous and dynamic communication environment has intensified the need for the reconfigurable protocol stack. In this paper, a novel architecture for the reconfigurable protocol stack is proposed, which is a unified specification of the protocol components and service interfaces supporting both static and dynamic reconfiguration for existing industrial communication standards. Within the architecture, a triple-level self-organization structure is designed to manage the dynamic reconfiguration procedure based on information exchanges inside and outside the protocol stack. Especially, the protocol stack can be self-adaptive to various environment and system requirements through the reconfiguration of working mode, routing and scheduling table. Finally, the study on the protocol of dynamic address management is conducted for the system of controller area network (CAN). The results show the efficiency of our self-organizing architecture for the implementation of a reconfigurable protocol stack.