In the system of systems (SoS) requirement modeling, the mission attribute is not used during the process of mission decomposition, so it is not easy to check the rationality of the decomposition. To solve the problems, this paper proposes an approach to SoS mission modeling and analysis based on the ontology. According to the key role of the mission in the requirement modeling of SoS, some attribute of the mission is defined, and the conceptual model of SoS mission is constructed. In order to make the decomposition of the mission more scientific and rigor ous, the mission decomposition algorithm is designed and the related attribute value of the mission is introduced in the decomposition process. By using the web ontology language description logic （OWL-DL） ontology reasoning and query technology, we make a formal analysis and verification of the constructed mission model by using the ontology reasoning engine Pellet to check whether the decomposition principle of the mission is decomposed to check the rationality of the decomposition.