Multiple ontology in the field of public health have been integrated to a comprehensive knowledge base for major public health emergencies, especially in decision-making. Based on the reuse of Vaccine Ontology, Human Disease Ontology, and Symptom Ontology, on one hand, the formal merging of ontology is completed with the help of Protégé ontology editing tool, and on the other hand, the semantic fusion of ontology is completed by using Word2vec and Owlready2 to achieve the overall fusion of multiple ontology in the public health domain. The experiments indicated that the comprehensive ontology constructed by this method has high accuracy of semantic relationships and represent knowledge in the public health domain from a multidimensional perspective, providing decision support in the process of effective response to the risk of major public health emergencies.