Floods are often caused by short-term heavy rainfall. An Integrated Flood Analysis System (IFAS) model is good at runoff simulation and a Long Short-Term Memory (LSTM) model is good at learning massive data and realizing rainfall forecast. In this paper, the applicability of the IFAS model to runoff simulation in the Tokachi River basin and the LSTM model to forecast hourly rainfall was studied, and the accuracy of flood prediction was also studied by inputting the optimal rainfall data forecasted by the LSTM model into the IFAS model. The research results show that the IFAS model can accurately simulate the runoff process in the Tokachi River basin. In the calibration period and the verification period, the Nash–Sutcliffe efficiency coefficient (NSE) of all simulation results are above 0.75; the LSTM model can achieve forecast hourly rainfall with high precision, the NSE of best forecast results is 0.86; the IFAS model can achieve flood prediction with high precision by using the optimal rainfall data forecasted by the LSTM model, the NSE of simulation result is 0.81. The above conclusions show that it is of great significance to combine the hourly rainfall forecasted by the LSTM model with the IFAS model for flood prediction.