The Yellow River Basin in Inner Mongolia (YRBIM) has witnessed major changes in land use/land cover (LULC), which have had an impact on the basin’s ecosystem, in the context of fast economic development and urbanization. This study set out to investigate the ecological risk and key driving forces in the basin as LULC evolves. In order to evaluate the ecological risk of the basin and use a geographic detector model to understand the causes of its spatial heterogeneity, we built a landscape ecological risk index (ERI) model based on changes in LULC from 1990 to 2020. The findings indicate that between 1990 and 2020, LULC modifications led to the transfer of several land types to a small number of land types, all of which have since changed into other land types. With high risk areas primarily located in the Hobq Desert, the Hetao irrigation area, and some portions of the Mu Us Sandy Land, the ecological risk level in the basin is gradually decreasing. Human activities are the main cause of the regional variation of ecological risk in the basin, with topography and climate coming in second and third. The Yellow River Basin’s ecological danger and environmental quality have only received a limited amount of analysis to date. This study is a crucial resource for the development of civilization and ecological restoration in the region.