Typhoon Morakot 2009, with significant southwest monsoon flow, produced a record-breaking rainfall of 2361 mm in 48 hours. This study hopes to improve a statistical typhoon rainfall forecasting method used over the mountain region of Taiwan via an artificial neural network based southwest monsoon enhancement (ANNSME) model. Rainfall data collected at two mountain weather stations, ALiShan and YuShan, are analyzed to establish the relation to the southwest monsoon moisture flux which is calculated at a designated sea area southwest of Taiwan. The results show that the moisture flux, with southwest monsoon flow, transported water vapor during the landfall periods of Typhoons Mindulle, Bilis, Fungwong, Kalmaegi, Haitaing and Morakot. Based on the moisture flux, a linear regression is used to identify an effective value of moisture flux as the threshold flux which can enhance mountain rainfall in southwestern Taiwan. In particular, a feedforward neural network (FNN) is applied to estimate the residuals from the linear model to the differences between simulated rainfalls by a typhoon rainfall climatology model (TRCM) and observations. Consequently, the ANNSME model integrates the effective moisture flux, linear rainfall model and the FNN for residuals. Even with very limited training cases, our results indicate that the ANNSME model is robust and suitable for improvement of TRCM rainfall prediction. The improved prediction of the total rainfall and of the multiple rainfall peaks is important for emergency operation.