Nitrogen losses from farmland, through improper drainage and rainstorm runoff, cause non-point source pollution and limit sustainable agriculture development. We determined the effects of controlled drainage (CTD) and conventional drainage (CVD) on migration responses, the transformation of nitrogen, and NH₄⁺-N and NO₃^--N losses. The results showed that four days after a rainstorm, compared with day one, NH₄⁺-N and NO₃^--N decreased by ranges of 28.7-46.7% and 7.5-47.5% in CTD, which was significantly higher than CVD. CTD also significantly reduced NH₄⁺-N and NO₃^--N losses in field drainage compared with CVD. NH₄⁺-N was reduced by 66.72% and NO₃^--N reduction was 55.56%. NH₄⁺-N contributed most to nitrogen losses, while NO₃^--N contributed less. Following rainstorm events, varying the water level using CVD and CTD had significant effects on NH₄⁺-N and NO₃^--N concentrations. The DRAINMOD-II model was used to simulate NH₄⁺-N and NO₃^--N levels. It indicated that the observed and simulated values of NH₄⁺-N and NO₃^--N concentrations in both CVD and CTD were fitted better. Lastly, the innovation of this study was that it focused on nitrogen concentrations and load changes in paddy field drainage after rainstorms, firstly using the DRAINMOD-N II model to simulate NH₄⁺-N and NO₃^--N concentration changes under field scale. It further validated the pollution-reduction effect under water level control in the paddy field. Also, it improved the irrigation-drainage system of paddy rice and provided a scientific basis for optimizing irrigation-drainage project design in rice irrigation district.