With the increasing number of large and medium-sized cities and the improvement of intercity transportation infrastructure, polycentric urban network is gradually emerging. Based on the strong link between urbanization and carbon dioxide emissions has been proven, using a panel data of 23 provinces of China over the period of 1997-2013, this paper explores the impact of polycentric structure on carbon dioxide emissions. The results reveal that there is a u-shaped relationship between polycentric structure and carbon dioxide emissions, and the relationship is obviously different between coastal and inland areas. At the same time, market integration can effectively reduce carbon dioxide emissions, and there is a substitution relationship between polycentric structure and market integration. In addition, urban distance and transportation infrastructure within provinces play a significant non-linear regulating effect on the relationship between polycentric structure and carbon dioxide emissions. The conclusion of this paper provides some empirical evidence for the coordinated development of China's future regional space planning and energy emission reduction.