We report a highly bright and stable aqueous dispersion of CuInS2/ZnS (CIS/ZnS) nanocrystals (NCs) using surfactant-assisted microemulsion and cold treatment. CIS/ZnS NCs were facilely synthesized via a stepwise, consecutive hybrid flow reactor approach. To stabilize the optical properties of hydrophobic CIS/ZnS NCs, cetyltrimethylammonium bromide (CTAB) was chosen as a matrix for aqueous phase transfer. As the result, a high quantum yield (QY) of 56.0% and excellent photostability were acquired in aqueous media. For removing excessive surfactants, cold treatment (4°C) of the CTAB-water solution was adopted to prevent further agglomeration of CIS/ZnS NCs, which could secure high stability over 6 months (less 2% reduction in QY). The optical features and structure of the obtained CTAB stabilized CIS/ZnS (CTAB-CIS/ZnS) NCs have been characterized by UV-vis and photoluminescence (PL) spectroscopies, XRD, XPS, EDX, and TEM. The high stability and PL of water soluble CTAB-CIS/ZnS NCs suggest their potential in nanoelectronics and bioapplications.