To address the problems of outdated management levels and low degree of intelligence in current waterlogged farmland areas, a digital twin-based management platform framework for waterlogged areas is proposed based on an analysis of key business requirements, taking physical waterlogged areas as units and business applications as driving forces. Using BIM+GIS, the Internet of Things (IoT) and UAV oblique photogrammetry, methods for constructing digital and visualized scenarios of waterlogged areas are developed. A three-level geospatial data foundation is established, a platform architecture consisting of sensing device layer, platform support layer, business application layer and user interaction layer is designed, and functional modules including a unified map of the waterlogged area, intelligent flood control and maintenance management are developed. A case study conducted in a waterlogged farmland area of the Sanjiang Plain shows that the proposed digital twin-based management platform realizes functions such as four pre-measures (forecasting, early warning, rehearsing, pre-planning) for flood control, farmland drainage and maintenance management, and improves the scientific and informatization levels of waterlogged area management, validating the rationality of the platform framework design and the feasibility of key technologies. This study provides a reference for the application of digital twin technology in waterlogged area management.