Fluorescence polarization template-directed dye-terminator incorporation(FP-TDI) is a simple, cheap and high throughput SNP (single nucleotide polymorphism) genotyping technology, but the quality of genotyping pictures cannot be evaluated, thus the reaction condition is very difficult to optimize. A numeric standard which can efficiently evaluate the SNP scoring picture was introduced, based on this standard, the reaction system was optimized. Using this method, randomly selected 337 SNP locus of human chromosome 3 were applied to high throughput SNP genotyping, the first time success rate reached 59.94%.