Ontology plays a key role in Semantic Web Service Registry (SWSR) which will add semantic information to web service. There exist some cases that users use different ontologies in the same domain to annotate web service. Therefore in this paper we present an approach to effectively manage the ontologies in SWSR based on ISO SC32 19763-3: MFI-3 (Metamodel Framework for Interoperability: Metamodel for Ontology Registration). We manage these different ontologies and the Same As relationship between them in order to maintain the semantic interoperability of web service based on these ontologies. Finally a prototype of Ontology Management Platform (OMP) is realized.