Multiternary quantum dots (QDs), because of the large degree of freedom in their structure and composition, have a wide tunability in their bandgap but also exhibit an increased uncertainty and complexity in their optical properties. In this work, we synthesized the ternary Cu-In-S (CIS) and quaternary Zn-Cu-In-S (ZCIS) QDs with different composition ratios via a facile aqueous route. The CIS QDs show multi-peak photoluminescence with their peak intensity dependent on the Cu : In ratio, which was illustrated using a donor-acceptor pair recombination process. Upon incorporation of Zn into the CIS QDs under similar conditions, the acquired ZCIS QDs exhibit blue-shifted photoluminescence (PL) spectra with an enhanced emission intensity and a narrowed spectral width (∼100 nm). A comparative study reveals that, reducing the Cu : In ratio in the CIS QDs and increasing the Zn content in the alloyed ZCIS QDs are both feasible strategies for bandgap engineering, although the influences on optical properties of the QDs were different. The XRD and EDX spectra revealed that the widening of the bandgap of the ZCIS QDs was correlated with the alloyed nanostructures and the preferential substitution of Cu by Zn. Compared to the Cu : In ratio variation, incorporation of Zn into CIS QDs is an effective strategy to achieve a more homogeneous absorption band and a wide range of emission wavelength tunability. After ZnS shell coating, the ZCIS/ZnS QDs show a further enhanced PL intensity with a prolonged fluorescence lifetime. Unlike CIS QDs, the blue shift in PL upon the shell growth was not pronounced for ZCIS QDs, for which a surface reconstruction mechanism was proposed and discussed. Finally, the as-prepared ZCIS/ZnS QDs were employed for in vitro cell imaging and exhibited good biocompatibility to macrophage cells.