Microreactors can be used for continuous operation and precise control of heating conditions in chemical synthesis. Therefore, microreactors are expected to offer a more efficient strategy for obtaining homogeneous nanocrystals and easier of size control than the general batch reaction system. CdSe nanocrystals can be turned into emission color by controlling the size of nanocrystals. In this study, we synthesized CdSe nanocrystals by a multiphase microreactor. The CdSe nanocrystals were coated with ZnSe and ZnS by using the multiphase microreactor. The nanocrystals are coated on their surface with a shell of a larger band gap semiconductor, which can improve luminescence efficiency. Furthermore, we investigated the residence time in relation to size of nanocrystals and optimized the coating layer thickness.