Rice is the most significant food crop in the world, but nitrogen and phosphorus runoff loss, a risk of pollution to adjacent water bodies, would occur during cultivation by unreasonable water and fertilizer management. Nitrogen and phosphorus runoff loss model for rice paddies is an effective way, in addition to assessing the risk of water pollution, to understand the spatial and temporal characteristics of regional water pollution discharge. Here, the authors expound the occurrence mechanism and key processes of nitrogen and phosphorus runoff loss in rice paddies, and then systematically reviews the research and development history of statistical empirical model, physical mechanism model, hydrological process model and ecosystem model. The authors point out that current models are limited by the uncertainty of nitrogen and phosphorus runoff losses in paddy fields, due to deficiency in the effective parameterization of the water-soil-air interface process, rationalization of model parameters based on high resolution, multi-year, multi-site and full flux, as well as regional-scale agricultural management (planting, fertilization, irrigation and drainage system) and the modularization of the joint control measures (distribution, scale, operation rules) of paddy-ditch-pond. Finally, the authors propose outlook on the establishment of high-resolution and full flux observation network for rice paddies' nitrogen and phosphorus cycles, regional data set research and development of agricultural management and control measures, integration and fusion of model development and advanced technological means, and multi-model integration of nitrogen-phosphorus-water coupling in rice paddies. Achieving these prospects will provide scientific support for the improvement of nitrogen and phosphorus runoff models for a rice paddy, the optimization of agricultural management measures, and the construction of climate-smart rice paddies.