The relationship between mountainous snowmelt runoff and temperature and rainfall was analyzed by using surface flow and climate data from the Juntanghu watershed, a typical study area for the central area of the northern Tianshan Mountains. Monthly temperature and precipitation data(1961-2010) observed from ten meteorological stations in the central area, including Wusu, Shihezi, Shawan, Manasi, Hutubi, Changji, Miquan, Xiaoquzi, Daxigou and Tianchi, were used for the Mann-Kendall trend analysis. The coefficient difference product curve was selected to analyze the relationship among temperature, runoff and precipitation. Hydrological modeling was conducted by using the soil and water assessment tool(SWAT). The parameters were calibrated by using the surface flow data(12 years) from the Hongshan Reservoir to predict the snowmelt runoff process of the Northern Tian Muontains in Xinjiang Wei Autonomous Region. Through changing the factors, such as average temperature and precipitation, results from sensitivity analysis demonstrated that snowmelt runoff was mainly affected by temperature and precipitation in snowmelt season. Moreover, from winter to spring, the effects of changing temperature were greater than those of precipitation on snowmelt runoff in the study area. This research leads to some potential contributions in understanding the mechanisms of snowmelt runoff in the warming central area of the Northern Tianshan Mountains.