A novel type of microcarrier was developed for optical encoding and fluorescence enhancement by depositing semiconductor quantum dots (QDs) on silica colloidal crystals beads (SCCBs). Monodisperse SCCBs were used as the support to deposit different-sized and different-layer QDs, thus leading to wavelength-and-intensity coding. The unique properties of QDs were well suited for multiplexed optical encoding, which could potentially yield a large number of codes. The SCCBs possess high porosity and high surface-to-volume ratio (SVR), which can provide stronger detection signals and thus high detection sensitivity. DNA hybridization studies demonstrated that the detection limit for this kind of microcarrier (6.7 pmol/L) was much lower than that for glass beads (890 pmol/L). These results indicate that designed optical encoding microcarriers could be successfully applied to high-throughput and multiplexed biomolecular assays.