Event-based runoff-pollutant relationships have been the key for water quality management, but the scarcity of measured data results in poor model performance, especially for multiple rainfall events. In this study, a new framework was proposed for event-based non-point source (NPS) prediction and evaluation. The artificial neural network (ANN) was used to extend the runoff-pollutant relationship from complete data events to other data-scarce events. The interpolation method was then used to solve the problem of tail deviation in the simulated pollutographs. In addition, the entropy method was utilized to train the ANN for comprehensive evaluations. A case study was performed in the Three Gorges Reservoir Region, China. Results showed that the ANN performed well in the NPS simulation, especially for light rainfall events, and the phosphorus predictions were always more accurate than the nitrogen predictions under scarce data conditions. In addition, peak pollutant data scarcity had a significant impact on the model performance. Furthermore, these traditional indicators would lead to certain information loss during the model evaluation, but the entropy weighting method could provide a more accurate model evaluation. These results would be valuable for monitoring schemes and the quantitation of event-based NPS pollution, especially in data-poor catchments.