Water-soluble AgInS2 quantum dots were synthesized via hydrothermal method using L-glutathione and sodium citrate as ligands. The effects of cation concentration, addition amount of ligands and pH values on the phase, morphology and fluorescence properties of AgInS2 quantum dots were systematically studied by X-ray diffraction, transmission electron microscopy, UV-Vis absorption spectra and photoluminescence spectra, respectively. The results showed that the particle size of AgInS2 quantum dots increased with the increase of cation concentration, which caused a systematic red shift from 614.7 nm to 675.6 nm in the photoluminescence spectra. Meanwhile, the Ag+ content in quantum dots decreased slightly due to the substitution of Ag+ by In3+, and the resulted defect of InAg could be served as the radiation recombination channel of excitons in AgInS2 quantum dots, which was propitious to improve its fluorescence emission efficiency. The fluorescence intensity of AgInS2 quantum dots reached to the maximum with the cation concentration of 0.7 mmol/L. Moreover, the ligands can effectively passivate the surface states and improve fluorescence properties of quantum dots. The AgInS2 quantum dots showed the strongest emission with the glutathione/Ag+ ratio at 20, and the sodium citrate/In3+ ratio at 7. The maximum quantum yields of AgInS2 quantum dots reached 10.1% due to the pronounced passivating effect on surface defects by ligands when the pH value of the solution was adjusted to 9, however the high pH values interfered with the combination between ligands and quantum dots, which induced a large number of surface non-radiative recombination defects, leading to the decrease of quantum yields. The infrared spectrometry results showed that glutathione and sodium citrate were mainly coordinated with AgInS2 quantum dots by the -SH, -NHR and -COO- groups. In addition, the surface of quantum dots was negatively charged, which demonstrates that the AgInS2 quantum dots possess good dispersibility and excellent chemical stability, showing wide application prospects in the biological imaging fields.