Water, energy, and carbon are critical resource and environmental elements that underpin socio-economic development. Exploring the coupling coordination among water-energy-carbon (WEC) and promoting their synergistic development are essential for advancing regional green and high-quality growth. Taking 95 cities in the Yangtze River Economic Belt (YREB) as the study area, WEC evaluation indicators were constructed from the dual-control perspective of total amount and intensity. The coupling coordination degree (CCD) model was applied to measure the CCD of WEC from 2006 to 2019, and the spatial durbin model was employed to identify the key influencing factors. The results showed that the CCD of WEC, water-energy, water-carbon, and energy-carbon in the YREB ranged from 0.6724 to 0.9987, and were classified into four levels: primary, intermediate, good, and quality coordination, with the median and mean showing an overall upward trend and notable improvement. Since 2014, more than 75% of the cities had reached the quality coordination level each year. All four categories of CCD exhibited positive spatial clustering, with cities achieving quality coordination in the other three categories evolving from scattered to contiguous distribution patterns, while energy-carbon remained widely distributed. Significant positive spatial spillover effects were detected for all four categories, indicating that improvements in local coupling coordination positively impacted that of spatially connected cities. Economic development level, environmental regulation, technological innovation, and NDVI significantly promoted local CCD, whereas fixed asset investment exerted a suppressing effect. Furthermore, economic development level and industrial structure upgrading showed positive and negative spatial spillover effects on spatially connected cities, respectively, while the negative spillovers of environmental regulation and technological innovation were more pronounced among geographically adjacent cities compared to economically linked cities.