Significance To analyze the characteristics of organ representation of anatomical ontologies, and to provide references for the research and construction of ontology in other fields. Method/Process The similarities and differences of three mainstream anatomical ontologies of SNOMED CT(SCT), Uberon and the foundational model of anatomy ontology(FMA) in terms of organ classification methods and term mapping are compared. Result/Conclusion Among the three main types of anatomical ontologies, SCT and Uberon are mainly classified according to the function of organs, while FMA is mainly classified according to the anatomical morphology of organs. The concept of organs in FMA and Uberon is the same as the concept of entire organs in SCT, and the representation forms of paired organs in SCT, Uberon and FMA are similar.