As twin pillars for mitigating the global climate crisis, the coupling coordination between urban resilience and low-carbon transition is of paramount importance. Using 48 cities across China’s three major urban agglomerations (2008–2022), this study applies the entropy-weighted TOPSIS method, Super-efficiency SBM, and coupling coordination degree models to measure the spatiotemporal evolution of urban resilience, carbon emission efficiency, and their coupling coordination (UCCD). A GeoDetector model is then used to identify the key determinants of UCCD. The findings show that (1) the carbon emission efficiency of the three urban agglomerations exhibits a declining trend followed by a resurgence, whereas urban resilience and UCCD demonstrate a fluctuating increasing trajectory. Significant geographical disparities exist in the three indices, with coastal and core cities exhibiting greater values than other urban areas. (2) Moran’s I result indicates a significant spatial positive connection in coupling coordination, with High-High aggregation predominantly observed in the Pearl River Delta, while Low-Low aggregation is primarily found in the Beijing-Tianjin-Hebei region. (3) The GeoDetector results of UCCD show clear stage evolution, shifting from fiscal balance and resource-based factors to innovation- and agglomeration-driven multi-factor synergy, with interactions moving from nonlinear-enhancement to dominant bi-enhancement. The findings herein offer a comprehensive basis for cities to pursue sound climate strategies, strengthen resilience, and advance regional cooperation toward sustainable low-carbon development.