A new method was developed for simultaneous determination of copper, lead, and cadmium, based on their voltammetric response at a carbon paste electrode modified with hexagonal mesoporous silica (HMS) immobilized quercetin (HMS-Qu/CPE). Compared with quercetin modified carbon paste electrode (Qu/CPE) and quercetin ionic liquid modified carbon paste electrode (Qu-IL/CPE), the HMS-Qu/CPE exhibited improved selectivity and high sensitivity toward the detection of copper, lead, and cadmium. The properties of the HMS-Qu/CPE in 0.1 M HCOONa-HCl buffer solution (pH 4.7) were investigated by adsorptive stripping voltammetry (ASV) and electrochemical impedance spectroscopy (EIS). The electrochemical behavior of copper, lead, and cadmium at the modified electrodes and factors affecting the preconcentration procedures were also investigated. Detection limits of 5.0, 0.8, 1.0 nM for copper, lead, and cadmium were obtained, respectively. The method is simple, fast, sensitive, and selective, and is successfully applied to soil sample.