The spatiotemporal variations of non-point source pollution from land use changes have significantly affected the surface water and groundwater quality of the basin. In this paper, Bahe River Basin, strongly affected by human activities, is chosen as an example, and the improved potential non-point source pollution index (PNPI) model was used, to quantitatively analyze the spatiotemporal variations and the main factors of potential non-point source pollution (PNP) risk affected by land use changes in arid area cities in the latest 20 years. The results showed that the main land use patterns in the Bahe River Basin were forest land and cultivated farmland, accounting for 85% of the total basin area. Urban area in the lower reaches of the river basin expanded nearly four times, encroaching on a large number of original grassland and cultivated land due to the strategy of regional integration development in Xi'an from 1995 to 2015. The Quantile classification method was applied to divide the PNPI risk grades into extremely low, low, medium, high and extremely high levels. The extremely high-risk area expanding rapidly as the urbanization in middle and lower reaches of the study watershed, while that the risk level of PNP reduced in the upstream after the water environmental protection measures. Urbanization in Xi'an City is the main reason for the rapid expansion of PNP areas with extremely high risk in the Bahe River Basin.