Low-carbon transition is of great importance in promoting the high-quality and sustainable development of urban agglomerations in the Yellow River Basin (YRB). In this study, the spatial Markov chain and Dagum’s Gini coefficient are used to describe the distribution dynamics and regional differences in the carbon emission intensity (CEI) of urban agglomerations in the YRB from 2007 to 2017. Additionally, based on the spatial convergence model, this paper analyzed the impact of technological innovation, industrial structure optimization and upgrading, and the government’s attention to green development on the CEI’s convergence speed for different urban agglomerations. The research results show that: (1) The probability of adjacent type transfer, cross-stage transfer, and cross-space transfer of the CEI of urban agglomerations in the YRB is small, indicating that the overall spatiotemporal distribution type of CEI is relatively stable. (2) The CEI of urban agglomerations in the YRB has decreased significantly, but the spatial differences are still significant, with a trend of continuous increase, and regional differences mainly come from the differences between urban agglomerations. (3) Expanding innovation output, promoting the optimization and upgrading of industrial structure, and enhancing the government’s attention to green development has a significant positive effect on the convergence rate of the CEI of urban agglomerations in the YRB. This paper holds that implementing differentiated emission reduction measures and actively expanding regional collaborative mechanisms will play an important role in reducing the spatial differences in carbon emissions in urban agglomerations in the YRB, realizing the goals of peak carbon and carbon neutrality.