Configuration design lies in the later stage of the conceptual design. It affects the downstream of design process and decides product structure. Therefore, it is necessary to pursue an approach to support such design stage activities. Port, as the location of intended interaction, plays an important role in the configuration design, which abstractly represents the intended exchange of signals, energy or material in a convenient way. Ontology is an unambiguous and flexible semantic specification corresponding entities, and it can effectively describe the function of port. In this paper, we firstly give port concept and port functional description, and their semantic synthesis is used to describe port ontology. Second, we build an ontology repository which contains the assorted primitive concepts and primitive knowledge to map the component connections and interactions. Meanwhile we provide a model of port-based multi-views which contains functional view, behavior view and configuration view, and gives the attributes and taxonomy of ports. Next, a port-based ontology language (PBOL) is described to represent the process of port ontology refinement, and a port-based FBS modeling framework is presented to describe system configuration. Finally, a revised tape case is given to show the application of the port-based ontology.