The meltwater released by the glaciers in the Aksu-Tarim Catchment, south of Tomur Peak (Central Tien Shan), feeds the Tarim River which is the main artery for the oases at the northern margin of the Taklamakan desert. The correct modeling of the contribution of the glaciers meltwater to the total runoff of the Tarim River is hampered by the lack of mass balance data. Multi-temporal digital terrain models (DTMs) allow the determination of volume changes for large samples of glacier. Here, we present the mass changes for 12 glaciers using 1976 KH-9 Hexagon, 2000 SRTM3 and 2009 SPOT-5 datasets. The results show that most of the glaciers have been losing mass since 1976. The largest glaciers, Koxkar and West Qongterang, lost − 0.27 ± 0.15 m w.e.a −1 and − 0.43 ± 0.15 m w.e.a −1 between 1976 and 2009, despite thick debris cover. However, some smaller glaciers show mass gain at their tongues indicating glacier surges. Using SRTM3 data the volume gain of Qinbingtan Glacier No. 74 could be dated to the time period 1999–2009. The overall mass budget of − 0.33 ± 0.15 m w.e.a −1 (for 1976–2009) of the investigated glaciers is within the variability range of the global average. However, in the recent years (1999–2009) a slightly decelerated mass loss of − 0.23 ± 0.19 m w.e.a −1 could be observed.