Flash droughts, characterized by their rapid onset and severe impacts on soil moisture and agricultural productivity, have garnered increasing attention in the context of global warming. In this study, the hydrological processes of the Yangtze River Basin (YRB) from 1961 to 2022 were reconstructed using the Variable infiltration capacity (VIC) hydrological model, integrating multi-source data such as meteorological records, vegetation cover, soil attributes, and digital elevation models. Based on flash drought identification criteria, the spatio-temporal characteristics of flash droughts was analyzed. Further, the response frequency and response time of gross primary productivity (GPP) and evapotranspiration (ET) was quantified. Our findings revealed that the frequency, intensity, and duration of flash droughts have significantly increased over the past two decades, with high-incidence areas primarily concentrated in the central basin, particularly in the Jialing River Basin, Hanjiang River Basin, and Dongting Lake basins. Meteorological analysis indicates that precipitation deficits were the dominant driver of flash droughts in the central and southern YRB, whereas temperature anomalies played a critical role in the northern and northwestern regions. Additionally, relative humidity and sunshine duration anomalies contributed to flash drought occurrence in specific sub-basins. The eco-hydrological responses varied across land cover types: croplands and grasslands exhibited higher GPP and ET response frequencies compared to forests, with over 90% of grasslands and 53.96% of croplands showing significant ET sensitivity to flash droughts. Response times also exhibited spatial and vegetation-type variations, with forests displaying shorter GPP response times but prolonged ET recovery periods. These findings deepened our understanding of the dynamic characteristics and ecological impacts of flash droughts in the YRB, providing crucial insights for drought monitoring, water resource management, and climate adaptation strategies in the region.