The invention provides a set of genes for head and neck squamous cell carcinoma (HNSCC) molecular typing. The set of genes comprises TP53 gene, CDKN2A gene, FAT1 gene, CASP8 gene, AJUBA gene, PIK3CA gene, NOTCH1 gene, KMT2D gene, NSD1 gene, HLA-A gene, HRAS gene, FBXW7 gene, RB1 gene, PIK3R1 gene, TRAF3 gene, NFE2L2 gene, CUL3 gene and PTEN gene. The invention also provides application of the genes in preparing a kit and gene chip for HNSCC molecular typing, and a kit and gene chip for HNSCC molecular typing prepared by using the genes. The genes can enhance the HNSCC typing rationality and accuracy, thereby providing key technical supports for implementing early diagnosis, effective interception and individualized treatment on HNSCC.