The invention discloses a carry-over storage year-end fluctuating level prediction method and system. The method comprises the following steps of: 1, establishing a carry-over storage year-end fluctuating level prediction model, and storing the carry-over storage year-end fluctuating level prediction model in a model library; 2, optimizing a scheduling target through a prediction server according to the maximum total cascade energy, and calculating and selecting a corresponding carry-over storage year-end fluctuating level prediction model; and 3, calling a model solution algorithm in an algorithm library through the prediction server, solving the carry-over storage year-end fluctuating level prediction model, and obtaining the year-end fluctuating level rule. Compared with the prior art, the method has the advantages that the solution process is simple, the benefits in the later scheduling period after the carry-over storage year-end are considered, and the accuracy of the prediction method can be improved; and compared with a BP neural network and other methods, the method is suitable for a reservoir with short runoff data series.