Runoff estimation in high-altitude glacierized basins is an important issue on the Tibetan Plateau. To investigate glacier mass balance, runoff and water balance in the Qugaqie basin and Zhadang sub-basin in the southern Tibetan Plateau, two glacier models and three snow models were integrated into the spatially distributed hydrological model JAMS/J2K. The results showed that the temperature index method simulated glacier runoff better than the degree-day factor method. The simulated glacier melt volume in the Qugaqie basin in 2006, 2007 and 2008 contributed 58%, 50% and 41%, respectively, to its total runoff. In the Zhadang basin, the glacier melt volume contributed 78% and 66% to its runoff during 2007 and 2008, respectively. Compared with the observation results, the simulated glacier mass balance showed similar variations with slightly higher values, indicating an underestimation of glacier melt volume. The water balance simulation in the upstream areas (705–874 mm) was comparable to that in the downstream areas (1051–1502 mm) and generally lower than the observed results. In both basins, the glacier mass-balance simulation was relatively accurate in the melt season compared to the other seasons.