The invention relates to a river channel water and sediment real-time prediction method based on data assimilation, and belongs to the technical field of water conservancy projects. The method includes the steps of firstly, collecting topographic data of a water channel to be predicated, upstream boundary condition data, downstream boundary condition data and fracture surface data of the river channel, setting up a one-dimensional non-steady-flow and non-balance sediment transport model, and solving the model; secondly, conducting water and sediment model assimilation on real-time observation data while receiving the real-time observation data, and enabling the assimilation value to serve as an initial field for calculation; thirdly, calculating the changes of the future water level, the further flow and the future sediment concentration according to information of the initial field and the boundary condition data. According to the method, the water level and flow speed prediction function, the flood forecast function and other functions are achieved on the basis of data such as the assimilation real-time water level, the flow speed and the sediment concentration, and the method has the advantages of being strong in pertinency, comprehensive in function, convenient to use, practical and the like, can be applied to river channel flood real-time forecasting of great rivers, and provides the decision-making support for the practical flood prevention command work.