The historical records of mechanical fault contain great amount of important information which is useful to identify the similar fault, but the structural representation and the knowledge reasoning problem are troubled that we use the historical records effectively. Aiming at the problem, the fault knowledge representation based on ontology is put forward out. Firstly, the knowledge characteristics, the ontology building significance and principle of fault are analyzed. Secondly, the fault ontology is defined and described. Finally, the applications of fault diagnosis ontology are studied in protégé. The case study shows that the fault knowledge representation based on ontology is very intuitive and efficient; it can provide us a novel way to deal with the fault diagnosis problem.