In the modern world of service-oriented software engineering (SOSE), the web services can be aggregated from the semantic interoperability level to meet the user’s personal and diversified needs. Firstly, the paper proposes a service clustering method based on service ontology and it clusters services from the aspect service function to form the service clusters. This can significantly reduce the overhead and enhance the service discovery efficiency. In addition, this paper makes use of the service capability and the interaction information to organize the service clusters form the semantic interoperability level. And it discusses the sufficient and necessary capability, and the type of interoperability. The users can discover the related services that can meet their needs efficiently. The corresponding algorithms are also designed. Finally, the effectiveness and feasibility of the proposed method are validated through experiments and a practical case study.