River habitat is an important component of river ecosystems and play an important role in maintaining river health. In order to clarify the habitat quality status of the Yellow River, the habitat status survey and habitat quality assessment of 26 sites from the source to the lower reaches of the Yellow River mainstream were carried out from May to July in 2021 and 2022. A total of 10 habitat indexes were selected from two aspects of river channels and riparian zones. The results showed that the comprehensive H scores of habitat quality of all sites of the Yellow River mainstream were between 79 and 153, and more than 69% of sites were in the medium grade. No significant differences in the habitat scores between 2021 and 2022, and among the source, upstream, middle and downstream were observed (p>0.05). Among the 10 habitat indexes, the scores of large woody residues were the lowest in the whole reach, ranging from 1-5. The water quality, human activity intensity, riparian vegetation coverage and riparian land use types showed significant differences among different regions (p<0.05). The results of principal component analysis showed that the main factors affecting the habitat quality of the Yellow River mainstream included riparian land use type, human activity intensity, water quality and riverbank stability. In future, ecological restoration and protection strategies should be put forward according to local conditions for the key influencing factors in specific regions of the Yellow River mainstream.