With the increase in the intensity and frequency of hydrological phenomena and the rapid development of social economy, direct economic losses caused by floods in China show an upward trend. In order to formulate disaster prevention and mitigation plans, adaptive strategies, and post-disaster compensation and recovery policies, it is important to comprehensively evaluate the economic losses caused by floods. Under the framework of multi-regional assessment, the environmental economic system model based on complex network and adaptive agents was used to simulate the daily indirect economic losses caused by regional floods in China transmitted through the industrial chain, such as floods in the middle reaches of the Yangtze River, floods in Dongting Lake Basin, floods in Songhua River, and the storm surge of Typhoon Tiange in 2017. The model shows the impact of the industrial chain and product shortage of all sectors in the regions concerned and reflects the early warning ability of the supply chain. The results show that the indirect economic loss in 2017 was 62.16 billion yuan, accounting for 29% of the direct economic loss, and more than 80% of the loss came from the manufacturing and service industries, which suffered no direct economic loss. The direct impact of flood disasters also spread to unaffected provinces through the supply chain, but most of the indirect economic losses mostly occurred in this local province, which may be related to the localized supply chain choice of enterprises. The indirect losses caused by work units’ direct impact in areas with developed manufacturing industries are higher, which may be related to their specific economic structures with high capital intensity and close inter-industry ties. Governments at all levels should increase their investment of adaptation funds in non-engineering measures to improve disaster resistance of the public and the carrier, set up flood insurance and risk compensation mechanisms to promote the recovery and reconstruction of disaster areas as soon as possible. Key regions and industries should carry out inventory reserve and capacity redundancy, to reduce the direct and indirect economic losses caused by floods.