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Hepatitis B is a major disease that causes serious public health problems worldwide. In this study, a visual DNA microarray was developed for the sensitive and specific detection of hepatitis B virus DNA (HBV-DNA) and its single nucleotide polymorphisms. 5′-End-amino-modified oligonucleotide, which was immobilized on microarray surface acted as capture probe, and another part of gold nanoparticles (AuNPs)-labeled oligonucleotide were designed to bind specifically with complementary targets HBV-DNA in the first place, and then linked as a single-strand DNA via Taq DNA ligase. The black image of microarray spots, resulting from silver stain on AuNPs, was used to visually detect target HBV-DNA and its single nucleotide polymorphisms. Capture probe with single base mismatch was prepared to detect the specificity and sensitivity of hybridization on microarray. Target HBV-DNA of different concentrations had been tested. The result indicated that this method has high sensitivity (ac. 10 pM) and specificity in the discrimination of single nucleotide polymorphisms. There is also an evident linear relationship between the signal intensity of microarray spots and the concentration of target DNA at the range of 10–100 pM. This visual detecting technique has great potential in clinical sittings because of its high sensitivity and good specificity.