This study conducts an empirical investigation into the decarbonization effects of urban polycentric structures, exploring their mechanisms and varied influences. Our findings reveal key insights. First, urban polycentric structures effectively reduce carbon emission intensity, a conclusion supported by robust tests and endogeneity analysis. Second, our analysis shows that polycentric structures significantly alleviate downtown overcrowding, reducing carbon emission intensity. These structures also impact carbon emissions through factors like labor allocation across industries and the entry of high-productivity enterprises. Third, our analysis shows that the impact of the polycentric structure on carbon emission intensity follows a ‘U-shaped’ pattern. In this ‘U-shaped’ pattern, the growth of an urban population scale can offset the potential negative impacts of this structure. Finally, government support, urban transportation networks, and communication technologies are crucial in enhancing the effectiveness of polycentric decarbonization. Our research contributes to the literature on polycentric structures and carbon emissions and offers policy implications for addressing climate change, applicable not only to China but also to other economies.