Since the ecological protection and high-quality development of the Yellow River basin in China have become a major national strategy, reducing carbon emissions has become pivotal. Therefore, based on the relevant data of 53 cities from 2008 to 2021 in seven urban agglomerations in the Yellow River basin, this paper explores the overall situation and spatio-temporal evolution of environmental governance and carbon emissions in the urban agglomerations in the Yellow River basin using the entropy method, ArcGIS, slacks-based measurement models (SBM models), etc. Additionally, this paper quantitatively analyzes the pathways by which environmental governance affects carbon emissions in the urban agglomerations in the Yellow River basin. The results show that carbon emissions increased year on year from 2008 to 2021, the growth rate slowed down gradually and exhibited a downward trend, and the largest amount of carbon was emitted in 2019, at 3495 million tons. Before 2017, the growth rate of carbon emissions showed a trend of increasing year by year, with the largest increase rate being 11.17% in 2010. After that, the growth rate of carbon emissions continued to decrease and entered a stage of fluctuation. The growth rate of carbon emissions in 2020 was the lowest, reaching −5.66%. The environmental governance effect of urban agglomerations in the Yellow River basin exhibits a large gap; the regional difference is obvious, and the overall trend is rising. Environmental governance has a significant negative effect on carbon emissions in urban agglomerations in the Yellow River basin. The cross-terms of environmental governance, the energy consumption structure, industrial structure upgrading, green technological innovation, and foreign direct investment (FDI) have significant negative impacts on carbon emissions, while the indirect impacts on urban agglomerations have shown regional heterogeneity. The goal of reducing carbon emissions in urban agglomerations in the Yellow River basin is being realized gradually. Based on research conclusions, policy suggestions are put forward, hoping to provide ideas for environmental protection and high-quality development of urban agglomerations in the Yellow River basin.