Abstract: Deep phenotyping is a precise and comprehensive approach used for the precise analysis and comprehensive assessment of multi-system phenotypes of the patients. The approach uses symptoms, signs, various medical examination and laboratory results, and other relevant medical information. In the clinical diagnosis and medical research of rare bone diseases, deep phenotyping plays a pivotal role. The realization of precision medicine primarily comprises three key dimensions: deep phenotyping, stratified medicine, and targeted therapy. The deep phenotyping is the basis for the latter two. Deep phenotyping not only facilitates fine subtyping of diseases, but also allows for the in-depth understanding of genetic data. The use of deep phenotyping requires stand- ardized terminology and specific procedures. Moreover, deep phenotyping shows substantial potential using the application of artificial intelligence technology particularly when combining with multi-omics techniques.