Purpose/Significance To elucidate the complex relationship among face phenotype-disease-gene, and to explore the underlying mechanisms of their interactions.Method/Process Based on scientific literature from the PubMed database, natural language processing tools and manual filtering methods are used to extract the knowledge of the concept and relationship of face phenotype-disease-gene reported in the existing literature, and a knowledge base is constructed. Result/Conclusion The study completes the framework design and construction of the knowledge base of the face phenotype-disease-genotype for intelligent health application, which lays a foundation of both data and theory for exploring the interplay between face phenotype-disease-gene, as well as the potential application of face phenotype in disease diagnosis.