The invention provides a flood forecasting system of a river system. The flood forecasting system comprises a river system setting module, a data acquiring module, a parameter calibration module and a forecasting system, wherein the river system setting module is used for setting the upstream-downstream topological relation of all sub-catchment of the river system; the data acquiring module is used for acquiring the real-time rainfall value and real-time flow value of all the sub-catchment of the river system and historical flood data during floods; the parameter calibration module is used for calibrating the parameters of a preset forecasting model according to the historical flood data; the forecasting module is used for acquiring a forecasting result of all the sub-catchment of the river system according to the upstream-downstream topological relation, the real-time rainfall value and real-time flow value of each sub-catchment, a preset future rainfall value, a preset upstream sub-catchment reservoir regulation manner of each sub-catchment and the parameter-calibrated forecasting model. By the flood forecasting system high in efficiency, flood forecasting can be performed on multiple sub-catchment of the river system.