The middle and lower reaches of the Yangtze River Basin occupy a strategically pivotal position in regional development; yet extreme drought-runoff events pose severe threats to water supply and ecological security. Despite this, systematic research gaps persist, including the lack of a unified definition, standardized identification criteria, and clear understanding of formation mechanisms for extreme drought-runoff. To address these limitations, this study focused on extreme drought-runoff in the basin, utilizing 1956–2024 discharge data from four mainstream hydrological stations and meteorological data from 171 stations. Quantitative discrimination criteria were established via Pearson-III frequency analysis; meteorological characteristics were analyzed using the Meteorological Drought Comprehensive Index; and formation mechanisms were explored through partial correlation analysis and multiple linear regression. This study innovatively proposed a basin-wide three-level quantitative discrimination criterion for drought-runoff based on the June–November flow frequency of key mainstream stations, which is distinguished from single-indicator drought identification methods (SPI/SPEI/SSI) by integrating basin-scale hydrological coherence and seasonal drought characteristics. The results revealed basin-wide extreme drought-runoff in 2006 and 2022, severe drought-runoff in 1972 and 2011, and relatively severe drought-runoff in 1959, 1992, and 2024. Typical extreme drought-runoff events were characterized by sustained low precipitation and high temperatures. Meteorological factors emerged as the primary driver during June–September, while reservoir operation and riverine water intake played secondary roles. Notably, the large-scale reservoir group in the Yangtze River Basin (53 key control reservoirs) helped alleviate drought-runoff impacts from December to May (non-flood season) via water supplementation. These findings provide a robust scientific basis for precise drought-runoff prediction and the development of targeted adaptation strategies in the Yangtze River Basin.