PCR-product microarray has great efficiency in SNP genotyping, mutation screening and epigenetic analyzing from a large number of samples. The current PCR-product microarray technology is mostly based on the 3-D gel microarray technologies due to its high loading capacity for PCR products, while there is little progress for PCR-product microarray on planar glass, which gives low background and convenient fabrication. In this study, we improved the PCR-product microarray on planar glass by employing a polyacrylic acid-covered slide. The raw amino-modified PCR products were simply precipitated with ethanol and directly spotted for DNA immobilization. Three detection methods of hybridization, solid-single base extension and solid-multiple bases elongation were carried out for single nucleotide variation identification on the PCR-product microarray. The experimental results showed that the high immobilization yield for raw PCR product was achieved, and the high specificity and high ratio of SIN for genotyping on the microarray were obtained. SNP genotyping of cytochrome P450 2D6 gene in 30 individuals was successfully demonstrated. This study has significantly increased the performances of PCR-product microarray, which could improve its applications in SNP genotyping and mutation screening in large number of individuals.