Cu doped Zn-In-S quantum dots (CZIS QDs) were synthesized by a hydrothermal method. The absorption and fluorescence peaks of CZIS QDs shifted monotonically to longer wavelengths with the increase of the Cu precursor and the decrease of Zn and In precursors. The dopant emission wavelength can be easily tuned in the whole visible region ranging from 465 nm to 700 nm by changing the molar ratio of Cu/Zn/In/S. On the basis of experimental results, it was testified that the emission of CZIS QDs was the trap state emission rather than the excitonic emission. The emission mechanisms of CZIS QDs were attributed to three kinds of approaches: (i) photogenerated holes efficiently move to trap states induced by Cu defects and recombine with the electrons in the energy level of sulfur vacancies; (ii) the holes in Cu trap states recombine with the electrons in the surface defect state; (iii) the electrons in the conduction band recombine with the holes in levels caused by Zn vacancies. After coating the ZnS shell around the CZIS core, the fluorescence quantum yield of CZIS QDs can reach 25-35%. CZIS/ZnS QDs conjugated with antibodies were successfully applied for labeling Hep-G2 liver cancer cells. The cytotoxicity studies revealed that the viabilities of the cells incubated with different concentrations of CZIS/ZnS QDs and at different times all remained at a high level of more than 90%. Hence, the CZIS/ZnS nanoparticle is a promising material as the fluorescent probe for biological applications.