Capillary electrophoresis (CE) and gold nanoparticle aggregation based-colorimetric detection (AuNP/ABCD) were incorporated to provide rapid, sensitive and selective detection of Cd2+, Pb2+, and Hg2+. CE and AuNP/ABCD were interfaced by a pressurized electric field decoupler to isolate the colorimetric reaction solution from the separation voltage. The AuNPs co-functionalized with 11-mercaptoundecanoic acid (MUA) and 6-mercapto-1-hexanol (MCH) were used as colorimetric probes, which provided enhanced sensitivity and good selectivity toward the heavy-metal ions. Under optimal conditions, good linearities were obtained for the analytes, and the detection limits for Cd2+, Pb2+, and Hg2+ were 0.214, 0.150, and 0.0214 μg/mL, respectively. The method was successfully applied to cosmetic samples, with recoveries of 87.8% to 103% for the heavy-metal ions spiked. Our results suggested the great potential of the CE-AuNP/ABCD strategy in determining heavy-metal ions in complicated matrices.