The glacier mass balance (GMB) is an important link between climate and water resources, which has remarkable regulation functions for river runoff. The research, using MOD11C3, TRMM 3B43 and other multi-source remote sensing data to drive the degree-day model, simulates the GMB processes and analyzes the recharge of glacial meltwater to runoff in the Manas River Basin (MRB) during 2000-2016. The results show that: (1) By constructing the temperature and precipitation inversion model, the accuracy of the meteorological remote sensing data can be effectively corrected, and the characteristics of climate change in the glacial region can be well described after downscaling. The annual average temperature and precipitation in the glacier area were -7.57 ℃ and 410.71 mm, respectively. The place at an altitude of 4200 m is a severe climate change zone. Above 4200 m, the temperature drop rates and precipitation gradients were -0.03 ℃/100 m and -2.66 mm/100 m, respectively; while below 4200 m, they were -0.57 ℃/100 m and 4.8 mm/100 m, respectively. Besides, at a higher altitude of 4700 m, the precipitation increased by 5.17 mm/100 m. (2) During the study period, the glaciers in the basin continued to be in a negative state, with a cumulative GMB of -9811.19 mm w.e. and an average annual GMB between -464.85 mm w.e. and -632.19 mm w.e. The vertical GMB increased by 244.83 w.e./100 m and 18.77 w.e./100 m in the ablation zone and the accumulation zone, respectively. From 2000 to 2002 and 2008 to 2010, the melting of glaciers slowed down, and the ablation was intensified from 2002 to 2008 and from 2010 to 2016. Strikingly, the loss of glaciers was most serious during the period 2005-2009. (3) The river runoff responded strongly to the change of GMB within the year, especially in July and August, namely, the GMB loss accounted for 75.4% of the total amount of the whole year, and the river runoff accounted for 55.1% of the annual total. The inter-annual glacial meltwater recharge rate fluctuated between 19% and 31%, which may be due to the differences of precipitation and snow melt water recharge rates in different years. The contribution rate of glacial meltwater of the MRB is close to that of other river basins on the northern slope of the Tianshan Mountains, which can further confirm the reliability of the GMB estimation results. Above all, the research can provide reference for the study of GMB in other river basins.