[Objective] The habitat quality of the urban agglomeration in the lower reaches of the Yellow River, and the relevant influencing factors were studied in order to provide a reference for ecological protection and quality development in the region. [Methods] The InVest model was used to analyze the evolution characteristics of regional habitat quality based on land use data from 2005 to 2020. The agglomeration effect of habitat quality was analyzed through spatial analysis. Influencing factors of habitat quality were determined using GeoDetector. [Results] ① From 2005 to 2020, the overall habitat quality of urban agglomeration in the Lower Yellow River basin was low, with an average value index of 0.402 2. During this period, habitat quality initially decreased and then increased. ② Spatial autocorrelation analysis showed that habitat quality was highly correlated, showing a polarized clustering pattern. Habitat quality showed a cluster of high values (H-H) in the western and northern parts of the Central Plains urban agglomeration and the central part of the Shandong Peninsula urban agglomeration, and a cluster of low values (L-L) in cities with more prominent economic development in the urban agglomeration, such as Zhengzhou and Qingdao City. ③ The results of the GeoDetector analysis showed that land use was the main factor influencing habitat quality of urban agglomeration in the Lower Yellow River basin, and that the interaction between different factors was stronger than the influence of individual factors on habitat quality. [Conclusion] Regions of urban agglomeration in the Lower Yellow River basin with high habitat quality should continue to protect the ecological environment, while regions with low habitat quality should strictly control land exploitation and the expansion of construction land, and improve land use efficiency.