Modeling, one of the main pillars of good scientific research, is a long-standing multidisciplinary activity to understand and analyze complex systems. In this paper, the focus is directed toward conceptual modeling of multi-terminal seaports specialized in handling and treatment of intermodal transport units (ITU). These systems are complex with highly dynamic and stochastic behaviors and actors, therefore, studying them as a coherent whole or just analyzing one part by taking into account the high degree of integration among the different aspects and actors linked by a flow of activities, information, and interactions is a bet lost in advance without a well-defined design process. Several design approaches and methodologies have been proposed over the years, but nonetheless, there is still no agreement on how to conduct modeling of complex systems because they are of different kinds. In this line, this paper proposes a top-down approach for container and Ro-Ro terminals largely inspired by the Unified Process Methodology and refined through several research projects that we have been involved in. It gives some recommendations and guidelines as well as a helpful way to successfully build modular and consistent simulation models. To prove its efficiency, it was applied to a case study and the resulting models were validated by the subject matter’s experts.