Partitioning operating systems (POSs) have been widely applied in safety-critical domains from aerospace to automotive. In order to improve the safety and the certification process of POSs, the ARINC 653 standard has been developed and complied with by the mainstream POSs. Rigorous formalization of ARINC 653 can reveal hidden errors in this standard and provide a necessary foundation for formal verification of POSs and ARINC 653 applications. For the purpose of reusability and efficiency, a novel methodology by integrating ontology and refinement is proposed to formally specify and analyze POSs in this paper. An ontology of POSs is developed as an intermediate model between informal descriptions of ARINC 653 and the formal specification in Event-B. A semiautomatic translation from the ontology and ARINC 653 into Event-B is implemented, which leads to a complete Event-B specification for ARINC 653 compliant POSs. During the formal analysis, six hidden errors in ARINC 653 have been discovered and fixed in the Event-B specification. We also validate the existence of these errors in two open-source POSs, i. e., XtratuM and POK. By introducing the ontology, the degree of automatic verification of the Event-B specification reaches a higher level.