The invention discloses an SNP (single-nucleotide polymorphism) detection method based on high-flux sequencing. The method comprises the following steps: designing probes, carrying out pre-amplification and biotin labeling, hybridizing, connecting, carrying out Barcode specific primer amplification, sequencing, and analyzing SNP site information of the sample according to the sequencing result. The experiment proves that the method enhances the sensitivity of the system, is simple in sample labeling, eliminates the influence of the non-specific amplification product in the pre-amplification so as to be beneficial to data analysis, is simple in the library establishment method, lowers the probability of template random mutation, greatly lowers the sequencing cost, is easy for data analysis, is flexible for site selection and is very suitable for large-scale sample screening on a medium quantity of mutant sites.