Based on the precipitation data of 6 automatic stations during 2013-2017 in the Yigeziya River Basin in Aktao county of Xinjiang and 7 national meteorological stations during 1961-2017 around the basin, the function relation between flood depth and rainfall was constructed by using FloodArea model in order to explore the threshold of disaster-causing critical rainfall under different recurrence periods of mountain flood. The hourly inundated area and inundated depth were simulated by hydrodynamic model. Combined with the disaster-affected factors (population distribution, GDP, land-use types) in the study area, the flood disaster risk zoning of the basin was completed. The results show that the middle and lower reaches of the basin was the high risk area of flood disaster risk, while the relatively high altitude area in the upper reaches of the basin was the low risk area of flood inundation.