The invention provides an SNP (single nucleotide polymorphism) genotyping method and an application thereof, and relates to an SNP genotyping method. The SNP genotyping method is an SNP genotyping technology based on the combination of restriction endonuclease fragment length polymorphism (RFLP) and a melting curve. The method is high in accuracy, good in stability, fast, time-saving, high-throughput and safe, facilitates automatic operation and doesn't require gel electrophoresis, the operation process produces no harm to a human body, and the cost is low. The SNP genotyping method not only gains a great success in the aspects of plant SNP genotyping and breeding of Chinese cabbage, Chinese kale, tomatoes and the like, but also has a great application value in the aspects of establishment of a high-precision genetic map, fine mapping of genes, genome-wide association analysis, establishment of a phylogenetic tree and the like in biology.