Located in the Tibetan Plateau, the upstream regions of the Mekong River (UM) and the Salween River (US) are very sensitive to climate change. The ‘VIC-glacier‘ model, which links a degree-day glacier algorithm with variable infiltration capacity (VIC) model, was employed and the model parameters were calibrated on observed streamflow, glacier mass balance and MODIS snowcover data. Results indicate that: (1) glacier-melt runoff exhibits a significant increase in both areas by the Mann–Kendall test. Snowmelt runoff shows an increasing trend in the UM while the US is characterized by a decreasing tendency. In the UM, the snowmelt runoff peak shifts from June in the baseline period 1964–1990 to May for both the 1990s and 2000s; (2) rainfall runoff was considered as the first dominant factor driving changes of river discharge, which can be responsible for over 84% in total runoff’ trend over the two regions. The glacial runoff illustrates the secondary influence on the total runoff tendency; (3) although the hydrological regime is rain dominated in these two basins, the glacier compensation effect in these regions is obvious, especially in dry years.