Megacity clusters are the key battlegrounds for carbon emission reduction in China, and the polycentric spatial structure of these clusters has a profound impact on their carbon emission intensity. This paper focuses on five major megacity clusters: the Beijing–Tianjin–Hebei (BTH), Yangtze River Delta (YRD), Pearl River Delta (PRD), the middle reaches of the Yangtze River (MRYR), and the Chengdu–Chongqing (CY) City Clusters. We construct an inter-period panel dataset spanning from 2002 to 2023 and utilize an index of polycentric spatial structure, which equally considers both morphology and functionality. A fixed-effects model is employed, and the Lind–Mehlum U-shape test is applied to identify the nonlinear relationship. Additionally, a two-step approach is used to examine the mediating effect of industrial agglomeration, while interaction terms help identify the moderating effects of technological innovation and transport infrastructure. The results indicate a significant U-shaped relationship between the polycentric structure of megacity clusters and carbon emission intensity. When the polycentric spatial structure index reaches a specific threshold, carbon emission intensity is minimized, suggesting that a moderate degree of polycentricity is most conducive to carbon reduction. Mechanism analysis reveals that industrial agglomeration functions as a significant mediator, whereas technological innovation and transport infrastructure serve as critical moderators in this relationship. Based on these findings, we propose several policy recommendations: to guide the moderate adjustment of the polycentric structure of city clusters with stage-specific targets, optimize the mechanism of industrial synergy and transfer, differentiate the allocation of innovation resources, and achieve a fine-tuned alignment between the transport system and spatial structure. These measures will support the high-quality, low-carbon transformation of city clusters.