The current urban development in cities along the Lower Yellow River is in tension regarding human–land relations. To achieve the goals of ecological protection and high-quality development (HQD), it is urgent to scientifically measure and analyse the region’s function development and development coordination (DC). This study focuses on cities along the Lower Yellow River, constructs a three-dimensional HQD assessment framework based on urban functions through multiple remote sensing data, and evaluates DCs by feature classification. The results show the following: (1) The HQD of the study area shows a trend of decreasing and then increasing during 2000–2020 and reaches its highest level at the end. HQD shows a spatial trend of decreasing from south to north and from east to west. (2) The overall agricultural function of the study area declined slightly; the ecological function declined first and then increased, with the highest value occurring in 2000; and the urban function increased steadily and improved significantly after 2015. (3) DCs under different administrative levels are polarised, with high-level DCs exhibiting a spatial leader effect. (4) Urban development preferences in the study area are divergent, and the functional type with the highest share under different administrative scales is agro-ecological, which is mainly influenced by differences in natural base. This study reveals the characteristics of HQD and functional changes in cities along the Lower Yellow River, combined with a hierarchical classification of DCs and the types of development preferences, providing a reference for the formulation of spatial governance strategies.