We propose a dynamic incidence matrix (DIM) for reflecting states and time conditions of a timed Petri net (TPN) explicitly. Since a DIM consists of a conventional incidence matrix, two time-related vectors and two state-related vectors, we can get the advantages inherent in the conventional incidence matrix of describing a static structure of a system as well as another advantage of expressing time dependent state transitions. We introduce an algorithm providing the DIM with a state transition mechanism. Because the algorithm is, in fact, an algorithmic model for discrete event simulation of TPN models, we provide a theoretical basis of model transformation of a TPN model into a DEVS(Discrete Event system Specification) model. By executing the algorithm we can carry out performance analysis of computer communication protocols which are represented TPN models.