This study employs a with-and-without comparison method to quantify the impacts of Xiangjiaba Reservoir’s varying outflows on the economic benefits of ship upsizing in the upper Yangtze River waterway from Yibin to Fuling. A navigation economic benefit model is developed based on reservoir topography and hydrological data, constrained by the waterway bearing capacity. By integrating typical route freight rates and vessel type datas, this study compares transportation costs under reservoir operation versus natural flow conditions and quantifies the economic benefits of ship upsizing. The results demonstrate that as outflow increases, particularly beyond the 3000 \(\textrm{m}^3/\textrm{s}\) threshold, waterway bearing capacity and shipping efficiency improve significantly, enabling larger vessels with lower unit costs. These findings provide theoretical support for optimizing reservoir operations to balance power generation and navigation while offering insights for navigation benefit assessments in other reservoir systems.