A semantic annotation method for Web database query result is proposed in this paper by adopting the deep annotation procedure in semantic Web. As a global schema Web database should be followed, domain ontology is introduced to the annotation procedure for a completed and consistent annotation result. The query interface and the query result features are analyzed in detail, the strategy of query condition reconfigured is adopted, and then the semantic markups of query result are determined. By collecting Web database from different domains, the experiments indicate that the approach proposed can annotate the Web database query result properly under the support of domain ontology.