Abstract: The Yellow River Basin, a critical region for China's ecological security and high-quality development, urgently requires a systematic analysis of the synergy between pollution reduction and carbon reduction (PCR) and its interaction with green technological innovation (GTI) and industrial structure upgrading (ISU). Using data from 53 prefecture-level cities in the Yellow River Basin (2013-2022), this study constructed a coupling coordination model to measure the synergy effect of PCR. It then integrated kernel density estimation, spatial autocorrelation analysis, and a panel vector autoregression (PVAR) model to reveal the spatiotemporal evolution of PCR synergy effect and systematically analyzed the interaction mechanism between PCR, GTI, and ISU. The results revealed that: (1) The PCR synergy effect exhibited an overall upward trend in cities of the Yellow River Basin, with an evident east–west gradient and a consistent spatial shift of the synergy center from Jinzhong to Lüliang. Though there was a convergence trend in the differences between cities, significant intra-regional disparities persisted in the middle and lower reaches. The synergistic governance of PCR demonstrated a cyclical pattern in its effectiveness. (2) All three subsystems (PCR, GTI, ISU) displayed strong path dependence, with GTI showing the highest inertia. (3) PCR synergy had a lagging inhibitory effect on GTI, while ISU played a dual driving role in the triadic system of "PCR, GTI, ISU". This study highlighted systemic challenges in the basin's collaborative governance, including differentiated synergistic effects, lagging industrial structural transformation, and barriers to technology diffusion. Accordingly, it proposed recommendations such as establishing a regionally differentiated PCR target system, implementing green technology innovation-driven incentive mechanisms, and fostering green industrial transition in old industrial cities, providing theoretical support and empirical evidence for promoting regional green transformation and high-quality development.