The Karakoram Mountains are well known for their widespread surge-type glaciers and slight glacier mass gains. On the one hand, glaciers are one of the sensitive indicators of climate change, their area and thickness will adjust with climate change. On the other hand, glaciers provide freshwater resources for agricultural irrigation and hydroelectric generation in the downstream areas of the Shaksgam River Basin (SRB) in Western China. The shrinkage of glaciers caused by climate change can significantly affect the security and sustainable development of regional water resources. In this study, we analyzed the changes in glacier area from 2000 to 2016 in the SRB using Landsat TM (Thematic Mapper)/ETM+ (Enhanced Mapper Plus)/OLI (Operational Land Imager) images. It is shown that the SRB contained 472 glaciers, with an area of 1840.3 km², in 2016. The glacier area decreased by 0.14%/a since 2000, and the shrinkage of glacier in the southeast, east and south directions were the most, while the northeast, north directions were the least. Debris-covered area accounted for 8.0% of the total glacier area. We estimated elevation and mass changes using the 1 arc-second SRTM (Shuttle Radar Topography Mission) DEM (Digital Elevation Model) (2000) and the resolution of 8 m HMA (High Mountain Asia) DEM (2016). An average thickness of 0.08 (±0.03) m/a, or a slight mass increase of 0.06 (±0.02) m w.e./a has been obtained since 2000. We found thinning was significantly lesser on the clean ice than the debris-covered ice. In addition, the elevation of glacier surface is spatially heterogeneous, showing that the accumulation of mass is dominant in high altitude regions, and the main mass loss is in low altitude regions, excluding the surge-type glacier. For surge-type glaciers, the mass may transfer from the reservoir to the receiving area rapidly when surges, then resulting in an advance of glacier terminus. The main surge mechanism is still unclear, it is worth noting that the surge did not increase the glacier mass in this study.