Snow is the most fast changing element in the cryosphere. A major proportion of flow in the Toxkan River is contributed by snowmelt runoff. The MODIS MOD10A2 remote sensing database of snow cover products from March 2000 to December 2012 was used to analyze the snow cover changes in the Toxkan River basin, one of the source regions of the Tarim River. It is shown that MODIS snow cover data is suitable of detection of spatial-temporal changes of snow cover across the basin and snow cover fraction has significant difference in temporal and spatial scale in the basin. In year with abundance of snow, snow cover fraction can reach more than 90% in January; but in less snow year, only 50%. Results show large variation in snow cover between 2000 and 2012 while an increasing trend is observed. Compared with other seasons, the increasing trend of snow cover is more obvious in winter. And compared with other elevation band, the increasing trend of snow cover over 3 000-4 000 m elevation band, which is the main snow cover distribution area, is more obvious. The Snowmelt Runoff Model (SRM) is used and forced with gridded temperature, precipitation and remotely sensed snow cover. The model is calibrated using monthly discharges from 2000 to 2004 and validated using monthly discharges from 2004 to 2006. It is shown that SRM can be used to simulate the stream flow in this basin with a certain degree of accuracy. There are no obvious differences for spring runoff simulation by using three RCP scenarios. In the future, spring runoff will increase significantly since April.