The invention of reconfigurable manufacturing systems (RMSs) has created a challenging problem: how to quickly and effectively modify an RMS to address dynamic changes in a manufacturing system, such as processing failures and rework, machine breakdowns, addition of new machines, addition of new products, removal of old machines, and changes in processing routes induced by the competitive global market. This paper proposes a new model, the intelligent colored token Petri net (ICTPN), to simulate dynamic changes or reconfigurations of a system. The main idea is that intelligent colored tokens denote part types that represent real-time knowledge about changes and status of a system. Thus, dynamic configurations of a system can be effectively modeled. The developed ICTPN can model dynamic changes of a system in a modular manner, resulting in the development of a very compact model. In addition, when configurations appear, only the changed colored token of the part type from the current model has to be modified. Based on the resultant ICTPN model, deadlock-free, conservative, and reversible behavioral properties, among others, are guaranteed. The developed ICTPN model was tested and validated using the GPenSIM tool and compared with existing methods from the literature.