Accurate precipitation prediction is of great significance for regional flood control and disaster mitigation. This study introduced a prediction model based on the least square support vector machine (LSSVM) optimized by the genetic algorithm (GA). The model was used to estimate the precipitation of each meteorological station over the source region of the Yellow River (SRYE) in China for 12 months. The Ensemble empirical mode decomposition (EEMD) method was used to select meteorological factors and realize precipitation prediction, without dependence on historical data as a training set. The prediction results were compared with each other, according to the determination coefficient (R2 ), mean absolute errors (MAE), and root mean square error (RMSE). The results show that sea surface temperature (SST) in the Niño 1 + 2 region exerts the largest influence on accuracy of the prediction model for precipitation in the SRYE (R2SST= 0.856, RMSESST = 19.648, MAESST = 14.363). It is followed by the potential energy of gravity waves (Ep) and temperature (T) that have similar effects on precipitation prediction. The prediction accuracy is sensitive to altitude influences and accurate prediction results are easily obtained at high altitudes. This model provides a new and reliable research method for precipitation prediction in regions without historical data. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.