This study presents a stable and controllable synthesis of fluorescent magnetic nanoparticles in a flow-through microchannel for the bimodal use of magnetic activated cells sorting and fluorescence-activated cell sorters. The La Mer process is carried out to synthesize magnetic nanoparticles using co-precipitation. Then, the magnetic nanoparticles are coated with conjugation of chitosan and fluorescent isothiocyanate with two different concentrations. The chemical composition of the magnetic nanoparticles is determined by comparing the standard X-ray diffraction peaks of Fe3O4, and their sizes are also examined by using field emission scanning electron microscopy and dynamic light scattering measurement. The magnetic property of saturation magnetization and coercive field is characterized in a vibrating sample magnetometer. Also, the possibility of external manipulation in the synthesis of the magnetic particles is demonstrated by separating the synthesized fluorescent magnetic nanoparticles into a non-reacting lamination flow. Finally, their fluorescence property is determined by measuring the fluorescence adsorption spectra and the photoluminescence emission spectra in UV-Vis spectroscopy.