Exploring the impact of population flow on carbon emissions in urban agglomerations against the background of urban innovation is of great significance for promoting regional low-carbon coordinated development and responding to climate change. Taking China’s three major urban agglomerations as the research object, this study introduces spatial factors to analyze the impact and mechanisms of heterogeneous population mobility on carbon emissions in the context of innovation. The findings reveal the following: (1) Carbon emissions in China’s three major urban agglomerations exhibit spatial correlation, and the spatial effects of different types of labor mobility on carbon emissions are complex. High-skilled labor flow helps reduce carbon emissions and mitigates the adverse impact of urban innovation on carbon emissions; low-skilled labor flow increases carbon emissions but is difficult to integrate with urban innovation, and the impact of urban innovation on carbon emissions does not change with the influence of low-skilled labor mobility. (2) There are significant differences in the spatial spillover effects of heterogeneous population flows on carbon emissions among China’s three major urban agglomerations. Due to the stronger administrative characteristics of the Beijing-Tianjin-Hebei urban agglomeration compared to other urban agglomerations, the spatial spillover effects of carbon emissions from heterogeneous population flows are not significant. In contrast, the Yangtze River Delta and Pearl River Delta urban agglomerations have relatively higher levels of integration, resulting in significant spatial spillover effects of carbon emissions from heterogeneous population flows. The article concludes by suggesting that institutional barriers hindering population mobility should be continuously removed, the positive interaction among cities should be activated, and the low-carbon development of urban agglomerations should be promoted.