Ontology matching can solve the heterogeneity problem between two ontologies, and EA represents a state-of-the-art technique for matching ontologies. However, there are two defects concerning the EA-based ontology matching technique: (1) a reference alignment between two ontologies to be matched is required in advance; (2) the confidence of entity similarity measure is low computational complexity of measuring the similarity value is high. To overcome these drawbacks, in this paper, an Evolutionary Algorithm with Context-based Reasoning method (EA-CR) is proposed, where: (1) an approximate metric without the reference alignment is utilized for evaluating the alignment’s quality; (2) a Context-based Reasoning method is presented to distinguish the heterogeneous entities. The experimental results show that the proposed approach is effective.