The present invention relates to a method for mapping heterogeneous medical data, the method comprising the steps of: generating domain clinic model ontology that defines a concept of arbitrary medical data collected from individual clinics and a relationship between the medical data; if SNOMED CT ontology that defines the concept and relationship of the domain clinic model ontology and standardized medical terms is loaded and the concept included in the domain clinic model ontology and/or the SNOMED CT ontology has a degree of similarity equal to or greater than a preset threshold value, determining that the concept has been mapped and generating a DCM-SNOMED mapping file for the mapping information; if vMR ontology describing the concept and relationship of data models defined by the SNOMED CT ontology and Health Level 7 standard is loaded and the concept included in the SNOMED CT ontology and/or the vMR ontology has a degree of similarity equal to or greater than a preset threshold value, determining that the concept has been mapped and generating a vMR-SNOMED mapping file for the mapping information; and generating a DCM-vMR mapping file for mapping information between the arbitrary medical data collected from the individual clinics and the concept included in the vMR ontology by using the DCM-SNOMED mapping file and the MR-SNOMED mapping file.