Achieving the synergistic effect of pollution reduction and carbon mitigation (PRCM) is a core pathway for promoting green and low-carbon transition and realizing the “dual carbon” goals, as well as a crucial mechanism for coordinating ecological environment governance with climate action. Based on panel data from three major urban agglomerations (Beijing–Tianjin–Hebei, Yangtze River Delta, and Pearl River Delta) between 2008 and 2019, this study employs network centrality and structural holes to characterize urban network positions (UNP), and systematically investigates the impact mechanisms and spatial heterogeneity of urban network positions on PRCM synergy using a dual fixed-effects model. The findings reveal that (1) urban network positions exert significant inhibitory effects on the overall synergy of PRCM, meaning higher centrality and structural hole advantages hinder synergistic progress. This conclusion remains valid after robustness checks and endogeneity tests using instrumental variables. (2) Heterogeneity analysis shows the inhibitory effects are particularly pronounced in Type I large cities and southern urban agglomerations, attributable to environmental governance path dependence caused by complex industrial structures in metropolises and compounded pressures from export-oriented economies undertaking industrial transfers in southern regions. Northern cities demonstrate stronger environmental resilience due to first-mover advantages in heavy industry transformation. (3) Mechanism testing reveals that cities occupying advantageous network positions tend to reduce environmental regulation stringency and research and development investment levels. Conversely, cities at the network periphery demonstrate late-mover advantages by embedding environmental regulations and building stable technological cooperation partnerships. This study provides a theoretical foundation for optimizing urban network spatial configurations and implementing differentiated environmental governance policies. It emphasizes the necessity of holistically integrating network effects with ecological effects during new-type urbanization, advocating for the establishment of a multi-scale coordinated environmental governance system.