Abstract Medium- and long-term runoff forecasting has always been a problem, especially in the wet season. Forecasting performance can be improved using complementary ensemble empirical mode decomposition (CEEMD) to produce clearer signals as model inputs. In the forecasting models based on CEEMD, the entire time series is decomposed into several sub-series, each sub-series is divided into training and validation datasets and forecasted by some common models, such as least squares support vector machine (LSSVM), and finally an ensemble forecasting result is obtained by summing the forecasted results of each sub-series. This model was applied to forecast the inflow runoff of the Shitouxia Reservoir (STX Reservoir). The forecasting results show that the Nash efficiency coefficient of the LSSVM model is 0.815, and the Nash efficiency coefficient of the CEEMD-LSSVM model is 0.954, an increase of 13.9%. The root mean square error value is reduced from 20.654 to 10.235, a decrease of 50.4%. The runoff forecasting performance can be effectively improved by applying the CEEMD-LSSVM model. When analyzing the annual runoff forecasting results month by month, it was found that the forecasting results for November to April were unsatisfactory compared results from the nearest neighbor bootstrapping regressive (NNBR) model, which was more suitable for the dry season, but the forecasting results for May to October improved significantly. This also proves that the CEEMD-LSSVM model has a great advantage in the forecasting of inflow runoff during the wet season. In the optimized operation of reservoirs, the forecasting result of inflow runoff in the wet season is more important than in the dry season. Therefore, when forecasting annual runoff month by month, the CEEMD-LSSVM model is recommended for the wet season combined with the NNBR model for the dry season.