Abstract: Frequent occurrence of the global flash drought has posed severe threats to regional agricultural production and food security in recent decades, leading to substantial yield reductions and increasing uncertainties in food systems. Therefore, it is of great importance to quantify the impacts of the flash droughts on crop yields in order to improve the drought risk assessment and agricultural adaptation. A few previous studies have statistically analyzed the temporal and spatial evolution of the flash drought events in the major grain-producing regions in China. However, it is still lacking in the fine-scale and process-based quantitation. Particularly, it is often required to consider the crop growth characteristics, phenological stages, and multiple interacting climatic factors. This study aims to assess the impacts of the flash droughts on crop yield and agricultural productivity using a crop model. Flash drought events were also identified in China during 1950–2022 using soil moisture reanalysis data. Multiple datasets were integrated, including the long-term climatic observations, soil properties, and crop-specific parameters. An AquaCrop model was established to simulate the responses of the major grain crops to various drought conditions. A “flash drought–phenology–yield” multi-scenario simulation framework was developed after the simulation. The temporal distribution of the crop phenological stages was explicitly incorporated to evaluate the yield responses to different drought intensities and durations. A systematic and spatially explicit assessment was performed on the evolution characteristics of the flash droughts and their impacts on the crop growth and yield in the diverse climatic zones. The results revealed that: 1) The calibrated AquaCrop model demonstrated high simulation accuracy, with coefficients of determination (R²) for maize, rice, and wheat reaching 0.91, 0.82, and 0.77, respectively. 2) There was a significant increase in the frequency of the flash drought events in the major grain-producing regions from 1950 to 2022, indicating an outstanding upward trend, particularly after the 1980s. The vegetative and reproductive growth stages were identified as the two most vulnerable periods for the flash drought occurrence, accounting for approximately 38.6% and 15.0% of the total events, respectively. 3) The yield losses induced by flash droughts were consistently higher than those by conventional slow-onset droughts within the growing season, with an average increase of about 10% in the yield reduction. Furthermore, the rice exhibited the highest sensitivity to the flash droughts, followed by maize, whereas the wheat was relatively less affected among the staple crops. Moreover, the reproductive growth stage was identified as the most critical period for the yield formation, indicating the most susceptible to flash drought stress (yield losses exceeding 47.10%). Overall, there was a quantitative assessment of the flash drought impacts on the crop yields. The crop phenology and rapid soil moisture depletion were then incorporated into the drought evaluation in the future. The “flash drought–phenology–yield” framework can offer a flexible approach to couple the flash drought dynamics with the crop growth simulations, thereby improving the accuracy of yield impact assessments under complex climates. Consequently, these findings can also provide a scientific basis to develop adaptive strategies, thus enhancing early warning on the agricultural risks with the increasing frequency and intensity of flash droughts.