Existing conceptual design methods mainly focus on component modeling and representation, which makes them insufficient to help in the conceptual design stage. Port ontology, as an approach to formally expressing product design, has been effectively applied to concept description of a product. An incidence matrix support for product conceptual design based on port ontology is given in this paper. It formally represents and organizes product information in both functional ontology and physical domain in a hierarchy. Port compatibilities are used to map and link the two components. This makes it possible to build incidence matrix and decompose it into an independence matrix, and allow designers from different backgrounds with various interests to access the design ontology. A multilevel matrix is constructed to generate principle schemes of products at different levels of abstraction, which facilitates design decision-making through the whole conceptual design stage. A case study is also given to demonstrate the proposed approach.