This study investigates the relationship between urbanization, innovation, and CO₂ emissions, with particular attention paid to the issue of how innovation influences the effect of urbanization on CO₂ emissions in urban agglomerations, considering the spatial spillover effect between cities. Therefore, based on panel data on 48 cities in the three major urban agglomerations in China from 2001–2015, a spatial econometric model is used to estimate the effect of urbanization and innovation on CO₂ emissions. The empirical results indicate that the relationship between urbanization and CO₂ emissions follows a U-shaped curve in the Beijing-Tianjin-Hebei (BTH), an N-shaped curve in the Yangtze River Delta (YRD) and an inverted N-shaped pattern in the Pearl River Delta (PRD). Additionally, innovation shows a significantly positive effect on reducing CO2 emissions in the YRD, but does not exert a significantly direct effect on CO₂ emissions in the BTH and the PRD. More importantly, innovation played an important moderating role between urbanization and CO₂ emissions in the YRD and PRD, suggesting that reducing the positive impacts of urbanization on CO₂ emissions depends on innovative development. In addition, urban CO₂ emissions presented a clearly negative spatial spillover effect among the cities in the three urban agglomerations. These findings and the following policy implications will contribute to reducing CO₂ emissions.