In order to analyze the impacts of water level changes on the ecological structure of water-level-fluctuating zone in the reservoir and improve the accuracy of the calculation of the inundation frequency, an analysis method of inundation frequency is proposed based on GF-1 satellite data. Firstly, the GF-1 WFV satellite imageries are preprocessed and a buffer zone is set up to extract the water body through multiple iterations. Then, the spatial distribution characteristics of the inundation frequency are obtained by geographical registration and inundation frequency calculated from the proposed method. Finally, the reliability of the inundation frequency is verified by the accuracy of water body distribution simulated from the method. The application in Sanhekou Reservoir show that the proposed analysis method of the inundation frequency can accurately reflect the spatiotemporal variation characteristics of the water body information. The overall classification accuracy and Kappa coefficient of simulated water body results reach 86.5% and 73% respectively, which can accurately reproduce the water body changes during the impoundment period of reservoir and improve the accuracy of inundation frequency calculation.