Since the Yellow River is a main source of water in Ningxia China, maintaining its healthy ecological environment is vital to Ningxia and the neighboring areas. Changes of land use caused by human activities such as population growth, urbanizing process, and industrial and mining construction would affect the balance and cycle of water in the Basin. Therefore, investigating hydrological responses of land use changes can provide insights into the characteristics and evolution of runoff the Yellow River Basin in the Ningxia section. This has imperative and practical significance to the rational use, allocation, and planning of water resources in a changing environment. In this paper, we analyzed the meteorological and hydrological elements of changing characteristics of the Yellow River Basin in the Ningxia section. Then we selected a distribution-based hydrology model of SWAT in combination with GIS to simulate annual and monthly runoff under different land use scenarios. Finally, we analyzed the influence caused by the changes of land use on runoff. We concluded that it is appropriate to lay a decision-making foundation to manage water resources of the Yellow River Basin in the Ningxia section.