Core/shell CdSe/ZnS quantum dots (QDs) are synthesized by a microfluidic reactor-assisted continuous reactor system. Photoluminescence and absorbance of synthesized CdSe/ZnS core/shell QDs are investigated by fluorescence spectrophotometry and online UV-Vis spectrometry. Three reaction conditions, namely; the shell coating reaction temperature, the shell coating reaction time, and the ZnS/CdSe precursor volume ratio, are combined in the synthesis process. The quantum yield of the synthesized CdSe QDs is determined for each condition. CdSe/ZnS QDs with a higher quantum yield are obtained compared to the discontinuous microfluidic reactor synthesis system. The maximum quantum efficiency is 98.3% when the reaction temperature, reaction time, and ZnS/CdSe ratio are 270°C, 10 s, and 0.05, respectively. Obtained results indicate that a continuous synthesis of the Core/shell CdSe/ZnS QDs with a high quantum efficiency could be achieved by isolating the reaction from the external environment.