In recent years, heavy rain and flood disasters occur frequently, which seriously hinders the operation of the supply chain system and causes huge economic losses. In this paper, the correlation characteristics of supply chain nodes are evaluated by the improved grey fuzzy OWA (Ordered Weighted Averaging) operator method. Then, the dynamic inoperable input-output model (DIIM) is used to simulate the time-dependent inoperable operation state of supply chain system under the influence of flood. On this basis, a case study was carried out on the manufacturing supply chain system affected by floods in Malaysia in 2021. Four indexes related to flood disasters and enterprise attributes were extracted to evaluate the disruption losses of the supply chain system. The results show that the function decline of each node of the supply chain caused by flood is affected by the interference of both the demand side and the supply side, and both the inoperability and the loss are a dynamic process. The simulation data intuitively showed the occurrence, diffusion and recovery process of supply chain disruption under floods. Therefore, it is convenient for decision makers to analyze and manage flood events and supply chain system operation.