—This paper addresses the simulation of the dynamics of complex systems by using hierarchical graph and multi-agent system. A complex system is composed of numerous interacting parts that can be described recursively. First we summarize the hierarchical aspect of the complex system. We then present a description of hierarchical graph as a data structure for structural modeling in parallel with dynamics simulation by agents. This method can be used by physiological modelers, ecological modelers, etc as well as in other domains that are considered as complex systems. An example issued from physiology will illustrate this approach.