Bias correction and spatial disaggregation (BCSD) is widely used in coupling general circulation models (GCMs) and hydrological models. However, there are some disadvantages in BCSD, such as only one GCM being selected, correcting biases through quantile-mapping (QM), and downscaling through interpolation. Then a combined approach of canonical correlation analysis filtering, multi-model ensemble, and extreme learning machine (ELM) regressions (CEE) was advanced. The performance of CEE and BCSD was evaluated with Manas River Basin as a study area. Results show it is unreasonable to correct biases through QM as it implies that the climate remains unchanged. Multi-model ensemble provides additional information, which is beneficial for regressions. CEE performs better than BCSD in temperature and precipitation rate downscaling. In CEE, the residual in temperature forecasting can be lower than 0.05 times temperature range and that in precipitation rate can be 0.33 times precipitation rate range. The performance of CEE in temperature downscaling in plains is better than mountainous areas, but for precipitation rate downscaling, it is better in mountainous areas. Increasing rate of temperature in the basin is 0.0254 K/decade, 0.1837 K/decade, and 0.5039 K/decade, and that of precipitation rate is 0.0028 mm/(day × decade), 0.0036 mm/(day × decade), and 0.0022 mm/(day × decade) in RCP2.6, RCP4.5, and RCP8.5, respectively.