Based on the Soil and Water Assessment Tool (SWAT) model, the monthly runoff processes of two land-use types in 2000 and 2015 were simulated in this paper. The relationship between runoff and landscape pattern was analyzed, and the spatial correlation between runoff and landscape pattern analyzed using the geographic weighted regression model combined with the change of landscape pattern in the study area from 2000 to 2015. The results show that: (1) The SWAT model can simulate the monthly runoff processes in the catchment area of the Ulungur River Basin (URB) under different land-use types for 2000 and 2015, but the simulation effect in 2000 was found to be better than that in 2015. (2) From 2000 to 2015, the area of woodland and grassland decreased. Runoff was positively correlated with woodland, grassland, largest patch index, mean patch area (AREA_MN), and contagion index, and negatively correlated with others. This indicates that the landscape fragmentation of URB was aggravated in 2000–2015, the landscape balance was destroyed, and the ability of rainfall interception and water conservation was weakened. (3) Landscape pattern indicators of grassland had a negative spatial impact on URB runoff, and the northern region of URB was more severely affected in 2015 than in 2000. AREA_MN landscape pattern index had a positive impact on runoff in the northern part of URB, and the positive impact in northern URB in 2000 was better than that in 2015.