In recent years, extreme rainfall events with short delays and heavy rainfall have often occurred due to severe climate change. In 2015, Typhoon Soudelor caused a short-delayed heavy rainfall event in Nanshih River, which caused damage to a section of the Lansheng Bridge discharge station. The section was relocated upstream to rebuild the discharge station in 2019. However, the new discharge station cannot measure high flow due to the bridge structure. The flow observation range of Lansheng Bridge is therefore limited to normal flow, making it impossible to accurately estimate the flow during high-water stages. The purpose of this study is to use the past flow data of Nanshih River to estimate the flow rate under different return periods using frequency analysis. We used a Digital Elevation Model (DEM) to map the river’s topography, and used the 3D hydraulic calculations of the FLOW-3D model to estimate the water stage and discharge of the Lansheng Bridge. We then verified the accuracy of the model with the measured flow and water stage, and finally used the water stage and discharge data obtained from numerical simulation to construct the stage–discharge rating curve of the Lansheng Bridge. In addition to preventing flood disasters, this study approach can provide reliable data for use in water conservation. It may also be utilized to overcome the problem of measuring and estimating high flow during typhoon floods.