This paper presents a novel approach to model a complex evolving system, a Digital Business Ecosystem (DBE) that takes the specific needs of Small and Medium-sized Enterprises (SMEs) into account. It aims to provide an open-source distributed environment to support the spontaneous evolution and composition of services forSMEs. A two-tier architecture model as a simplified version of the system is presented, consisting of a business network layer and a P2P communication layer that interact with each other and evolve over time. The benefit of the model-driven approach is to allow us running discrete event simulations on it to study, e.g how the topology of the SME network affects the topology of the P2Pcommunication network.