The factors that influence the colorimetric gene detection of gold label silver stain and improve the detection signals were studied. The influence of amino DNA probes and thiol DNA modified gold nanoparticles was investigated based on a sandwich hybridization system. An increase in amino probe concentration brought about an increase in hybridization signal which reached a threshold corresponding to the saturated concentration of amino probes bounded onto a glass slide surface. Since the steric hindrance effect of nanoparticles was dominant over the influence of a surface area, the bigger gold nanoparticles led to weaker hybridization signals. The hybridization efficiency enhanced significantly with the increase of the thiol DNA modified nanoparticle concentrations. Experimental results showed that 125 μmol/L of the amino DNA probe concentration, 15 nm of the gold nanoparticle diameter, and 4.07 nmol/L of the thiol DNA modified gold nanoparticle concentration were optimal for the detection system. The hybridization signals can be improved remarkably by choosing optimal hybridization conditions.