A two-step approach including the assembly of QDs and subsequent Stöber synthesis has been developed to encapsulate hydrophobic CdSe/Cd(x)Zn(1-x)S core/shell QDs into SiO2 beads. TEM observation shows that the core/shell QDs have high concentration in the SiO2 bead. The fabrication mechanism was proposed for these SiO2 bead. First, partially hydrolyzed tetraethyl orthosilicate (TEOS) replaces the initial ligands of the QDs and assembles the QDs into seeds by condensation reaction. 3-mercaptopropyltrimethoxysilane (MPS) was applied to control the assembly process and inhibit a heavy aggregation. Second, the mixed silane TEOS/carboxyethylsilanetriol sodium (CES) was used for Stöber process. The carboxyl group of CES can react with the sulfhydryl of the MPS facilitating the deposition of the SiC2 on the QDs seeds. Sonication was required for the formation of well-dispersed and well-coated SiO2 beads. The combined application of MPS and CES, the decent silane concentration, and the sonication during the Stöber process were crucial for the synthesis of SiO2 beads with high concentrated QDs.