Precipitation is one of the most important factors affecting the accuracy and uncertainty of hydrological forecasting. Considerable progress has been made in numerical weather prediction after decades of development, but the forecast products still cannot be used directly for hydrological forecasting. This study used ensemble pro-processor (EPP) to post-process the Global Ensemble Forecast System (GEFS) and Climate Forecast System version 2 (CFSv2) with four designed schemes, and then integrated them to investigate the forecast accuracy in longer time scales based on the best scheme. Many indices such as correlation coefficient, Nash efficiency coefficient, rank histogram, and continuous ranked probability skill score were used to evaluate the results in different aspects. The results show that EPP can improve the accuracy of raw forecast significantly, and the scheme considering cumulative forecast precipitation is better than that only considers single-day forecast. Moreover, the scheme that considers some observed precipitation would help to improve the accuracy and reduce the uncertainty. In terms of medium- and long-term forecasts, the integrated forecast based on GEFS and CFSv2 after post-processed would be better than CFSv2 significantly. The results of this study would be a very important demonstration to remove the deviation of ensemble forecast and improve the accuracy of hydrological forecasting in different time scales.