Researches for susceptibility of complex diseases need large-scale SNPs genotyping across many individuals. It leads to a requirement for a simple, cost effective, automatic and high-throughput genotyping method. Herein, a novel high-throughput SNP genotyping method using magnetic particles (MPs) in situ PCR and universal tags was described. PCR products were directly amplified by MPs in situ PCR and interrogated by hybridization with wild and mutant tagged probes and a pair of dual-color (Cy3, Cy5) universal detectors to determine SNP, and then genotype of each sample can be simultaneously identified by scanning the microarray printed with the denatured detectors on an unmodified clean glass slide. Morever, a pair of given dual-color universal detectors can be applied to any SNP loci by hybridization with allele specific tag probes. In this study, this new method have been applied to the analyze the methylenetetrahydrofolate reductase (MTHFR) gene C677T polymorphism in 96 different samples. The fluorescent ratios (match/mismatch signal) of homozygous samples were over 4.5, whereas heterozygous samples had ratios near to 1.0. The genotyping results were additionally validated by sequencing. By using universal tags and in situ magnetic particle PCR, this simple and cost-effective approach can be widely used in high-throughput SNP genotyping.