Abstract: Controlled drainage in paddy fields contributes to rainwater retention and runoff reduction, which is significant for preventing soil and fertilizer loss and mitigating channel flooding. However, the influence of controlled drainage height on water, sediment, and phosphorus transport processes in channels remains unclear. Taking the Gaoyou Irrigation District in Jiangsu Province as a case study, a coupled mathematical model for field-channel water, sediment, and phosphorus transport was established to investigate the reduction effects of different controlled drainage heights on channel water level, sediment concentration, and phosphorus concentration under various rainfall conditions. Results showed that, compared with conventional drainage (30 mm), the reduction effects significantly improved with increasing controlled drainage height (low storage, 50 mm; medium storage, 100 mm; high storage, 150 mm) under the same rainfall conditions. For the 2-year rainfall event, the three schemes reduced peak water levels in channels by 5%, 14%, and 31%, reduced peak sediment concentrations by 10%, 24%, and 67%, and reduced peak phosphorus concentrations by 5%, 15%, and 50%, respectively. Under the same controlled drainage conditions, the reduction effects gradually weakened with increasing rainfall return periods. For the high-storage scheme, the water level reduction rate decreased from 31% for the 2-year return period to 15% for the 50-year return period, while sediment and phosphorus reduction rates decreased from 67% and 50% to 34% and 24%, respectively. A quantitative relationship between controlled drainage height and reduction effects was established. With increasing storage capacity ratio, the channel flood peak reduction rate showed an“S-shaped” variation, while sediment and phosphorus reduction rates both showed linear relationships, with optimal reduction effects achieved when the storage capacity ratio was in the range of 0.6–0.8. These research findings provide a scientific basis for the design and optimization of drainage engineering in high-standard farmlands. The coupled model integrated three interconnected modules: a paddy-field rainfall-runoff module based on a single-layer tank model that simulated surface overflow, lateral seepage, and infiltration; a one-dimensional channel hydrodynamic and sediment-transport module built on the Saint-Venant equations and the sediment continuity equation; and a phosphorus migration module describing the exchange of dissolved and particulate phosphorus between the overlying water and suspended sediment. A field observation experiment conducted in a 125 m² paddy plot during a typical rainfall event was used to calibrate and validate the model, and the parameters were optimized using the SCE-UA algorithm. The Nash-Sutcliffe efficiency coefficients of the three key processes, namely water level, sediment concentration, and phosphorus concentration, all exceeded 0.75, while the channel hydrodynamic module achieved an NSE greater than 0.85, indicating that the simulated results agreed well with the measured data. Four rainfall return periods of 2, 10, 20, and 50 years were combined with four drainage heights of 30, 50, 100, and 150 mm to evaluate the reduction effects under different hydrological conditions. The results further revealed that increasing the controlled drainage height enhanced field water storage, delayed and reduced runoff generation, and thereby attenuated the peak discharge entering the channel, which was the primary mechanism responsible for the simultaneous reduction of peak water level, sediment concentration, and phosphorus concentration. The storage capacity ratio between the available field storage and the rainfall depth governed the reduction performance: when this ratio was lower than 0.6, the available field storage was insufficient to intercept rainfall during the peak period, resulting in limited reduction effects, whereas a ratio of 0.6–0.8 achieved the optimal performance. The channel flood-peak reduction rate increased in an S-shaped manner with the storage capacity ratio (R²=0.952), while the sediment and phosphorus reduction rates exhibited nearly linear relationships (R²=0.716 and 0.727, respectively). Therefore, increasing the controlled drainage height to 60%–80% of the expected rainfall depth can effectively enhance the reduction performance and provide practical guidance for the design and operation of drainage systems in high-standard farmlands.