Measuring the semantic similarity between pairs of terms in Gene Ontology (GO) can help to compare genes that can not be compared by other computational methods. In this study, we proposed an integrated information-based similarity measurement (IISM) to calculate the semantic similarity between two GO terms by taking into account multiple common ancestors that they share, and aggregating the semantic information and depth information of the non-redundant common ancestors. Our method searches for non-redundant common ancestors in an effective way. Validation experiments were conducted on both gene expression dataset and pathway dataset, and the experimental results suggest the superiority of our method against some existing methods.