Megacities in the Yangtze River Economic Belt (YREB) are facing severe challenges and unbalanced development. Combating megacity syndrome is crucial for achieving modernization. This study developed a Development-Autonomy-Inclusiveness governance framework to characterize megacity governance capacity modernization (MGCM). The integrated model is employed to evaluate the MGCM for nine megacities along the YREB in China from 2013 to 2022. The key determinants are identified by Geo-detector. The configuration pathways and synergistic mechanisms for high MGCM are depicted using fsQCA. The empirical study indicates that: (1) The MGCM is at a low level but displays a slight upward trend, with development capacity > autonomy capacity > inclusiveness capacity. The MGCMs of three urban agglomerations manifest as being development-driven, autonomy-constrained, and autonomy-promoted. (2) The synergistic interaction among determinants is greater than any single factor. (3) Megacities exhibited distinct pathways to achieve high MGCM: tri-capacity synergy pattern in the Yangtze River Delta, development dominant pattern in Chengdu-Chongqing, autonomy weakness pattern in the Mid-Yangtze River, and adversity survival pattern during extraordinary periods. A novel theoretical framework and practical examples are proposed for boosting the modernization of governance capacity in China’s megacities, offering valuable insights for advancing the governance modernization of megacities worldwide.