The invention discloses a flight mass spectrometry genotyping detection method. The method comprises the following steps: (1) designing three oligonucleotide probes for a SNP site, wherein the 3/endsof a first probe and a second probe are respectively two allelic genes, i.e., allele-specific oligos (ASOs) of a pre-selected SNP site, (2) when the sequence is completely matched with the target sequence, preparing a connection product, (4) carrying out enzyme digestion on the PCR product by using restriction endonuclease, and purifying the product by using streptavidin-coated beads, and (5) transferring the purified product to a 384-well chip. SNP site typing is carried out by adopting MALDI-TOF mass spectrometry, and SNP typing is provided by adopting the method which is simple to operate,low in cost and high in resolution ratio.