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Natural habitats are damaged by human interference to varying degrees during the urbanization process, which can impede a region’s high-quality development. In this study, we examined the spatial–temporal evolution characteristics of habitat quality and urbanization in the Lower Yellow River from 2000 to 2020 using the integrated valuation of ecosystem services and tradeoffs (InVEST) model and the comprehensive indicator method. We also evaluated the coupling relationship between the habitat quality and urbanization using the coupling coordination degree model. The findings indicate the following aspects: (1) Between 2000 and 2020, the Lower Yellow River’s habitat quality was typically mediocre, with a steady declining trend. The majority of cities displayed a trend toward declining habitat quality. (2) Both the urbanization subsystem and the urbanization level in 34 cities have demonstrated a consistent growth tendency. The urbanization level is most affected by economic urbanization among the subsystems. (3) The coupling coordination degree have revealed an ongoing trend of growth. In most cities, the relationship between habitat quality and urbanization has been evolving toward coordination. The results of this study have some reference value for ameliorating the habitat quality of the Lower Yellow River and solving the coupling coordination relationship between habitat quality and urbanization.