This study investigates anomalous precipitation patterns in the Taihu Basin, located in the Yangtze River Delta of eastern China, using high-resolution daily data from 1960 to 2019. Leveraging a deep learning autoencoder and self-organizing map, three spatially distinct types are identified—north type (72%), south type (19.7%), and center type (8.3%). The north type exhibits a pronounced upward trend (+0.11 days/year, p < 0.05), indicating intensifying extreme rainfall under climate warming, while the south type displays a bimodal temporal structure, peaking in early summer and autumn. Composite analyses reveal that these patterns are closely associated with the westward extension of the Western North Pacific Subtropical High (WNPSH), meridional shifts of the East Asian Westerly Jet (EAJ), low-level moisture convergence, and SST–OLR anomalies. For instance, north-type events often coincide with strong anticyclonic anomalies and enhanced moisture transport from the Northwest Pacific and South China Sea, forming favorable convergence zones over the basin. For flood management in the Taihu Basin, the identified spatial patterns, particularly the bimodal south type, have clear implications. Their strong link to specific circulation features enables certain flood-prone scenarios to be anticipated 1–2 seasons in advance, supporting proactive measures such as reservoir scheduling. Overall, this classification framework deepens the understanding of atmospheric patterns associated with flood risk and provides practical guidance for storm design and adaptive flood risk management under a changing climate.