Accurate runoff inversion is essential for watershed hydrology and water resources management, yet traditional single-model approaches often exhibit substantial biases in complex terrain and nonlinear flow regimes. This study presents a fusion modeling framework for the Jialing River Basin, combining three individual methods—the relationship fitting method, the improved Manning’s formula, and the C/M signal method—through weighted averaging, Bagging–AdaBoost, and Stacking ensemble strategies, with linear regression as a meta-learner for multi-source feature integration. Validation using monthly data from 2015–2020 shows that the Stacking-based model achieves superior performance (Nash–Sutcliffe efficiency = 0.981; RMSE = 38.69 m 3/s; RRMSE = 5.09%), outperforming both Bagging–AdaBoost and weighted averaging. The model effectively reduces systematic errors and variance, providing stable predictions across high- and low-flow regimes. These results demonstrate that ensemble-based fusion models significantly enhance runoff reconstruction and capture flow dynamics more accurately than individual approaches. The proposed framework offers a robust, scalable tool for hydrological estimation in complex basins and has important implications for water resources management and flood mitigation.