ABSTRACT Climate change and human activities have posed serious threats to fish diversity globally. Protecting favourite fish niches and identifying their drivers for spatial‐temporal change can effectively regulate the intensity of human activities and adapt to climate change. However, previous research on the driving factors for spatial and temporal niche change is rarely reported, severely limiting the efficiency of regulation and adaptation. Therefore, this paper presents a new framework to explore possible factors driving the change of fish niche. Based on 12 large‐scale field in situ sampling data from 2014 to 2018 and 2023, a dominance model was firstly used to screen dominant fish. Secondly, niche models of width and overlap were used to calculate fish niches, and MK mutation point test was used to determine mutations of fish and habitat relationship. Then, the correlation between habitat factors and fish density in biomass was determined with the help of CCA. Finally, a partial correlation analysis model was used to identify key driving factors. Results showed that there are nine dominant species, and in the areas with high water temperature in middle and low latitudes, Cyprinus carpio might become the fish species with the largest niche breadth. The key factors driving niche change of the dominant fish in the lower Yellow River are nitrate, total nitrogen and chlorine. What is worth noticing is that water temperature and dissolved oxygen may be key drivers for fish that survive in cold environments. Annually, the factors having the greatest to least influence on the niche of dominant fish were hydrological, water quality physical and water quality chemical factors. For hydrological factors, the dominant fish have the largest niche breadth in summer and the largest niche overlap in spring. For water quality physical factors, dominant fish have the largest niche breadth and the largest niche overlap in summer. For water quality chemical factors, the dominant fish have the largest niche breadth in summer, and niche overlap remains stable between seasons. Upstream and downstream fish niches differ significantly in mountain rivers with weirs. Hydrological factors have the greatest impact on niches of dominant fish in rivers with poor river network connectivity. Water quality indicators have the greatest impact on niches in heavily polluted watersheds. This study can provide a scientific basis for the conservation of fish diversity and ecological restoration in the Yellow River Basin. It can also provide reference and guidance for similar river basins around the world to cope with climate change, regulate human activities and enhance biodiversity.