Water–soluble CdSe:Zn/ZnS core-shell quantum dots were successfully synthesized in aqueous solution by a green synthetic route using a variety of ligands, and the effects of ligands on the structure and optical properties of the quantum dots were explored through a variety of analytical methods. XRD results show that the obtained CdSe:Zn/ZnS core-shell quantum dots possess cubic sphalerite structure of ZnS phase and their average grain size is about 2.4 nm, which is smaller compared with that of sample fabricated without ligands. SEM result shows that the shape of CdSe:Zn/ZnS is nearly spherical. Interestingly, the synthesized samples have good hydrophilicity, and the surfaces of the samples are coated with hydrophilic groups, which is consistent with the FT-IR results. Compared with the corresponding bulk materials, the absorption peaks of the quantum dots display a significant blue shift, demonstrating the obvious quantum confinement effect.