Ontologies become increasingly a foundation of each design process. Their application in system and process modeling is a new and insufficiently studied approach which has prompted in the present study. On the basis of detailed survey of theories and methods, therein an integrated methodology is proposed, founded on general system and process theories and Semantic Web technologies. The methodology includes methods and tools for meta-ontologies, and following domain, application and task ontologies of abstract and concrete system and process development. The purpose of elaborated ontological models is to better study, analyze, implement, document, communicate and reuse real systems and processes. A model of knowledge management system for ontology based system and process design is developed in order to demonstrate the potential and effectiveness of proposed methodology.