The impact of changing land use and land cover (LULC) on regional habitat quality have attracted extensive attention. The Loess Plateau is an ecologically fragile area; LULC changes in this region have complex impacts on habitat quality at multiple spatiotemporal scales. This study developed an integrated assessment method based on multi-source data to assess habitat quality changes in the Loess Plateau during recent years (2000-2015) and in the future (2015-2050) under four typical scenarios. A significant increase in urban land use was observed on the Loess Plateau from 2000 to 2050, which resulted in a continuous decrease in the cropland area. The area of forest and grassland landscapes was also reduced by both urban and cropland expansion, with the most significant loss in the grasslands. A future overall decreasing trend in overall habitat quality is predicted, but the SSP1-2.6 scenario is significantly better than the SSP5-8.5 scenario. Urban expansion contributes a rapidly increasing proportion of habitat quality decline on the Loess Plateau; urban land will become the most significant threat to regional habitat quality by 2030. Policies for socio-ecological protection with clear, high-level objectives can effectively promote habitat quality. It is recommended that national nature reserves be delineated and ecological functions in the study area be continuously monitored. This research provides a potential socio-ecological baseline and implementation strategy for the habitat conservation-oriented management of large and fragile ecological regions.