Magnetic nanoparticles (NPs) have been recognized as useful nanomaterial in the field of bio separation, because it is easy to handle the biological samples by applying magnetic field. In particular, multifunctional nanocomposites consisting of magnetic NPs and other functional NPs such as quantum dots(QDs) can be promising separation tools which exhibit valuable functions. Herein, QDs-assembled iron oxide-silica NPs (Fe2O3@SiO2@QDs NPs), which have both magnetic and fluorescent properties were prepared. The structure of Fe2O3@SiO2@QDs NPs is a core-shell type, which has magnetic NP in the core of silica backbone, and hundreds of QDs at the silica surface. The cells containing these NPs can be separated by magnetic field, while traced optically by bright fluorescence from the NPs. Moreover, the cells can also be separated by fluorescence-activated cell sorting(FACS) system. We demonstrate that these multifunctional NPs have a great potential in cell-separation.