During June to July, 2020, persistent heavy precipitation in the Yangtze River Basin (YRB) is resulting in extensive flooding, with over 158 fatalities and tremendous economic losses. This year’s disastrous flooding extreme is exceptionally different from those of other years. It contains over 1000-year return period events (for 30-day cumulative precipitation) as observed in Anhui, Guizhou and Sichuan Provinces. The mean precipitation is 308 mm in July 2020, being 54 mm higher than that of July 1998, when serious floods affected the entire Basin causing tremendous socio-economic consequences. Compared with 1998, the short-term (e.g., 1 day) precipitation in YRB did not show significant increases, while the long-term (e.g., 30 days) cumulative precipitation increases significantly. The highest observed 30-day cumulative precipitation is 1221 mm (in Anhui Province) in 2020, while the highest one in 1998 was 1028 mm (in Jiangxi Province). We thus find that this persistent heavy precipitation is the main cause of flooding in 2020. At the same time, TGR may mitigate up 43% of upstream flood, although the main contributors to this year’s YRB flood are in the middle and lower reaches. Affected by COVID-19, the number of people at risk in the threatened area are increased, and their capacities to mitigate the dual impacts of COVID-19 pandemic and flooding are hindered since (a) the flooding-caused mitigations may limit people’s ability to prevent from virus spreading, and (b) the pandemic is retaining a large amount of migrant workers being within YRB and subject to flooding impacts. Overall, our main discovery is that, although the short-term precipitation in YRB did not increase significantly in 2020, the cumulative one increased significantly in 2020.