An ontology is a state-of-the-art knowledge modeling technique in the natural language domain, which has been widely used to overcome the linguistic barriers in Asian and European countries’ intelligent applications. However, due to the different knowledge backgrounds of ontology developers, the entities in the ontologies could be defined in different ways, which hamper the communications among the intelligent applications built on them. How to find the semantic relationships among the entities that are lexicalized in different languages is called the Cross-lingual Ontology Matching problem (COM), which is a challenge problem in the ontology matching domain. To face this challenge, being inspired by the success of the Genetic Algorithm (GA) in the ontology matching domain, this work proposes a Compact GA with Annealing Re-sample Inheritance mechanism (CGA-ARI) to efficiently address the COM problem. In particular, a Cross-lingual Similarity Metric (CSM) is presented to distinguish two cross-lingual entities, a discrete optimal model is built to define the COM problem, and the compact encoding mechanism and the Annealing Re-sample Inheritance mechanism (ARI) are introduced to improve CGA’s searching performance. The experiment uses Multifarm track to test CGA-ARI’s performance, which includes 45 ontology pairs in different languages. The experimental results show that CGA-ARI is able to significantly improve the performance of GA and CGA and determine better alignments than state-of-the-art ontology matching systems.