The glacier mass balance (GMB) is an important link between climate and water re-sources and has remarkable regulatory functions in river runoff. To simulate changes of the GMB and to analyze the recharge rates of glacier meltwater to runoff in the Manas River Basin (MRB) during 2000-2016, MOD11C3, TRMM 3B43 and other multi-source remote sensing data were used to drive the degree-day model. The results showed that: (1) the accuracy of the remote sensing meteorological data can be corrected effectively by constructing the temperature and precipitation inversion models, and the characteristics of glacial climate can be finely described through downscaling. The average annual temperature was −7.57 °C and the annual precipitation was 410.71 mm in the glacier area of the MRB. The zone at an altitude of about 4200 m was a severe climate change zone, and above and below that zone, the temperature drop rates were −0.03°C/100 m and −0.57°C/100 m, respectively, while precipitation gradients were −2.66 mm/100 m and 4.89 mm/100 m, respectively. (2) The overall GMB was negative with a cumulative GMB of up to −9811.19 mm w.e. and the average annual GMB fluctuated between −464.85 and −632.19 mm w.e. Besides, the glacier melted slowly during 2000–2002 and 2008-2010, but rapidly for 2002–2008 Sand 2010–2016, while the most serious loss of the glacier occurred in 2005-2009. Moreover, the vertical changes of the GMB increased at 244.83 mm w.e./100 m in the ablation zone but only at 18.77 mm w.e./100 m in the accumulation zone. (3) The intraannual runoff strongly responded to the change of the GMB especially in July and August when the loss of the GMB accounted for 75.4% of the annual loss, and when runoff accounted for 55.1% of the annual total. Due to differences in the annual precipitation and snow meltwater outside the glacier, the interannual glacier meltwater recharge rates fluctuated between 19% and 31%. The recharge rate of glacier meltwater to runoff in the MRB was close to that for other basins in the Tianshan Mountains, which may be used as a basis to confirm the reliability of the estimated GMB results. Furthermore, based on the present findings, it is recommended that the research community pursue studies on the GMB in other alpine river basins.
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