The Juntanghu River Basin in the north Tianshan Mountain was chosen as the study area. A double-layer distributed snowmelt runoff model based on the principle of energy balance and mass balance was developed through digital elevation model (DEM) of the study area watershed information extraction and the world soil database and the national land-use data sets for watershed soil and land cover types of data. The analysis show that the measured and simulated runoff hydrograph in 2009 and 2010 fit the high QR passing rate of 87% and 90.85%. In addition, the combination of snow water equivalent changes in the value of MODIS data is verified to demonstrate the reliability of the model. The model is very useful and will provide a good example for snowmelt flood warning.