Abstract: From the viewpoint of system theory, the concept of complex large system for flood disaster is put forward, and some aspects of its characteristics such as high dimension, dynamics and complexity are discussed. Based on the comprehensive methodology with qualitative and quantilative integration, the comprehensive methodology of flood disaster analysis such as simulation, forecasting and evaluation as well as decision are investigated. Therefore, it will provide the scientific basis for investigating the methodology for the management and control on flood disaster, and it is helpful for improving the relationships among resource and environmant as well as social development.