Multicolor encoded beads were achieved by incorporating two color core-shell quantum dots (QDs) (CdSe/ZnS) to commercial polystyrene (PS) beads. By controlling the concentration ratios of the two quantum dots (QDs) in doping solutions, a series of codes with different intensity ratios were obtained. Based on the multiple encoded carboxylic modified polystyrene beads, fluorescent dyes labeled antibodies were distinguished successfully on the beads' surface. It suggests that the encoded beads from this method have the practicability in biological applications and chemical analysis.