Although there has been considerable computer-aided conceptual design research, most of the proposed approaches are domain specific and can merely achieve conceptual design of energy flows-processing systems. Therefore, this research is devoted to the development of a general (i.e., domain-independent) and knowledge-based methodology that can search in a wide multidisciplinary solution space for suitable solution principles for desired material-flow processing functions without designers' biases toward familiar solution principles. It first proposes an ontology-based approach for representing desired material-flow processing functions in a formal and unambiguous manner. Then a rule-based approach is proposed to represent the functional knowledge of a known solution principle in a general and flexible manner. Thereafter, a simulation-based retrieval approach is developed, which can search for suitable solution principles for desired material-flow processing functions. The proposed approaches have been implemented as a computer-aided conceptual design system for test. The conceptual design of a coin-sorting device demonstrates that our functional representation methodology can make the proposed computer-aided conceptual design system to effectively and precisely retrieve suitable solution principles for a desired material-flow processing function.