Based on Landsat MSS/TM/ETM+/OLI images of 1978,1991,2001,and 2015,glacier boundaries in the Shaksgam River Basin, Karakoram Mountains were extracted using computer aided image classification and visual interpretation methods, and the changes of glaciers in the study area were analyzed. The results show that the total area of glaciers in the study area was reduced from 1821.70 km~2 to 1675.92 km~2 during 1978-2015, by 145.78 km~2, or 8% of the total area of glaciers. Under the background of climate warming, however, the rate of glacier retreating shifted from fast to slow in nearly 40 years. In the study area, the glacier retreat rate on the southeastern aspect was significantly higher than on the northwestern aspect. Glacier retreat rate decreased with the increase of scale of glaciers. There were 27 typical glaciers that clearly progressed during 1978-2015,with areas and lengths significant increased. Among these, the velocity of change for the western side of the Wood stark glacier was 904 m/a during 1996-1998, the velocity of change for the eastern side of the K2 glacier was 446 m/a during 2007-2009,and the velocity of change for the 5Y654D497 glacier was 238 m/a during 1978-1990,respectively. These three glaciers seem to be the surge-type glacier. By analyzing the climate records and glacier variation in the study area, it was concluded that higher temperatures led to the glacier retreat of the study area, but increasing rainfall to some extent inhibited glacier retreat. Topographic condition and the scale of glacier were key factors for glacier changes as well.