Annually 5–6 typhoons strike the Yangtze Estuary (YE) as extreme events. However, their high energy and importance for sediment transportation and geomorphic changes are still not fully understood. In this study, high-resolution observations of wind, wave, flow velocity, and suspended sediment concentration (SSC) at two in-situ stations were carried out during the 2022 Hinnamnor typhoon. Additionally, we simulated the change in SSC, estuarine bed erosion/deposition, and flow and sediment transport with and without a typhoon in the YE using MIKE3 numerical model. The findings revealed that the Hinnamnor typhoon-induced waves increased the SSC of the turbidity maximum zone (TMZ) by a factor of 5.6 times (maximum is 2.8 kg/m3). The TMZ area also extended by 2.68 times (maximum is 7880km2, 70.4% of YE) in the YE. Moreover, the typhoon caused a dramatic change in sediment transport and bed erosion/deposition in the YE. First, in the delta front area where the mean water depth is >5 m, the typhoon significantly increased the southward flux of residual flow and sediment, causing sediment transport into Hangzhou Bay to abruptly increase 26.3 times (increase of 52 million tons, accounting for 1/3 of the present annual flux of the Yangtze River (150 million tons)) during a single spring-neap period. The net erosional area and volume extended to 6770km2 (60.4% of YE) and 91.18 × 106 m3. Second, in the delta shoals (where the mean water depth is <5 m, including east Chongming Shoal, Hengsha Shoal, Jiuduansha Shoal, and east-south Nanhui Shoal), residual flow and sediment flux decreased northward from the typhoon and resulted in the erosion of the shoal. Third, in channels with trumpet-shaped mouths (North Branch (NB), North Channel (NC) and South Passage (SP), except for North Passage (NP)), the upward flux of residual flow and sediment increased due to the typhoon, resulting in bed deposition in these channels (NB, NC and SP). This study highlights the important influence of typhoons on flow and sediment transport and bed erosion in estuarine areas.