In this study, the riverbank inundation caused by moderate frequent flooding events (with recurrence periods of less than 20 years), along with the increasingly serious hazards of backward flows in dike-through drainage ditches in the Ningxia Reach of the upper Yellow River (NRYR), were investigated. Then, a comprehensive method for hazard assessment of the floodplains and backward flows in the NRYR was proposed, which fully integrated geographical information systems (GISs), remote sensing (RS), and a digital elevation model (DEM), as well as river dynamics theory. This study first established a one-dimensional unsteady hydrodynamic model for the NRYR. The historical flood hydrology observation from 2012, along with the aerial image measurement data of the study area, were used to calibrate and verify the accuracy of the model. The hazards of riverbank inundation and damages to water affected engineering facilities, as well as the backward flows of dike-through drainage ditches caused by the moderate frequent flooding events, were comprehensively analyzed. Also, this study configured the hazard map and proposed revisions to the flood hazard ranking regime definitions, and discussed the impacts and prevention and control measures of moderate frequent flood damages. The proposed method could effectively meet the hazard analysis demands of the moderate frequent flooding events in the NRYR.