To inspire designers to do creative design more effectively, the classification and mapping relation in scientific principle knowledge were analyzed, and an application process for scientific principle knowledge in product innovation was proposed and established. According to the construction principle of domain ontology, the ontology vocabulary of function and effects were extended, and the representation model of scientific principle knowledge was presented and implemented with OWL. A software prototype of ontology-based scientific principle knowledge management system was developed according to the proposed theory, and then the construction mechanism and semantic retrieval technology of the system were discussed. Finally, an example was given to illustrate the system’s effectiveness.