Besides direct damages, flood have indirect impacts on cities, an essential one being on transportation. Flooded road closures cause absences and delays for employees, with cascading impacts on business and community. This study estimates the indirect losses from commuting delays caused by flooding in the coastal megacity of Shanghai. Our framework includes modeling of commuting patterns, flood hydrodynamics, and wage loss. The results show that the commuting pattern in Shanghai exhibits core-periphery and multi-core interactions. Flood events in Shanghai significantly disrupt urban mobility and incur substantial economic losses. Average vehicle speeds decrease by 28 % to 54 % across 1/10-year, 1/100-year, and 1/1000-year flood scenarios, dropping as low as 22 km/h during the most severe floods. Accessibility is heavily impacted, with 47 % to 92 % of commuter connections lost due to 51 to 186 traffic zones becoming inaccessible. Economic losses range from US$3.7 billion to US$12 billion, with the highest losses concentrated in the central districts of Xuhui, Jingan, Huangpu, and Hongkou, where the dense commuter population and concentrated economic activities make them particularly vulnerable. Our analysis also indicates that climate change exacerbates the decline in commuting accessibility, leading to even greater economic and social disruptions in the future. The findings have significant implications for risk management and adaptation, and the methodology can be used to assess commuter delay losses from flooding in other coastal megacities.