Hydrophobic CdSe/Cd0.5Zn0.5S core-shell quantum dots (QDs) with high photoluminescence (PL) efficiency and tunable PL have been fabricated through a controlled two-step synthesis. The size of CdSe cores depended strongly on the injection speed of trioctylphosphine selenium and reaction temperature and time. With increasing size, the morphology of the cores varied from spherical to rod. A Cd05Zn0.5S shell coating resulted in a high PL efficiency up to 80% and tunable PL spectra from green to red. Because resulting core/shell QDs exhibited narrow PL spectra (full-width at half-maximum of less than 30 nm) and high PL efficiencies, they were surface-modified by a SiO2 layer with functional groups for biological applications through a controlled reverse micelle route. Partially hydrolyzed tetraethyl orthosilicate (TEOS) play an important role for the QDs transferred into water phase from oil phase. The thickness of SiO2 layer was adjusted less than 5 nm through controlling the amount of TEOS and reaction time. Aminopropyltrimethoxysilane were added to attach functional groups on the SiO2 layer of the QDs. The functional SiO2-coated QDs were conjugated with immunoglobin G (IgG) antibody by using small molecules as cross linkers. Because the QDs revealed a high PL efficiency up to 30% after conjugation with IgG, they will have important applications in biological and medical research fields.