The achievement of China’s low-carbon development and carbon neutrality depends heavily on the decrease of manufacturing carbon emissions. From coagglomeration’s dynamic evolution perspective, by using panel-threshold-STIRPAT and mediation-STIRPAT models, this study examines the relationships among industrial coagglomeration, green innovation, and manufacturing carbon emissions and explores the direct and indirect function mechanisms. Panel data of China’s 30 provinces from 2010 to 2019 are employed. The results imply that, first, the impact of industrial coagglomeration on manufacturing carbon emissions is nonlinear and has significant threshold effects. Industrial coagglomeration negatively affects manufacturing carbon emissions, and as the coagglomeration level deepens, the negative effect has a diminishing trend in marginal utility. Once the coagglomeration degree exceeds a certain threshold, the negative impact becomes insignificant. At present, for 90% of China’s regions, an increase in industrial coagglomeration level can help reduce manufacturing carbon emissions. Second, green innovation is a vital intermediary between industrial coagglomeration and manufacturing carbon emissions. It is a partial intermediary when industrial coagglomeration is at a relatively lower-level stage and a complete intermediary when industrial coagglomeration is at a relatively higher-level stage. These findings reveal the significance of optimizing industrial coagglomeration and the level and efficiency of green innovation to decrease carbon emissions.