[Objective] The Jinsha River Basin is an important ecological area in the southwestern mountainous gorge region. Predicting and assessing climate and future runoff changes in the Jinsha River Basin under the background of global warming is of great significance for soil and water conservation, flood control, disaster reduction, and water resource planning at the basin scale. [Methods] This study simulates the hydrological processes of the Jinsha River Basin using the VIC model and downscales data from 20 climate models and the Multi-Model Ensemble Average (MMEA) under two emission scenarios (SSP2-4.5, SSP5-8.5) from the CMIP6 global climate models to predict runoff trends from 2015 to 2100. [Results] (1) The historical runoff simulation indicates that the Nash efficiency coefficient between the simulated and observed values exceeds 0.6, and the absolute value of BIAS is controlled within 0.15, demonstrating that the VIC model is suitable for simulating the hydrological process in the Jinsha River Basin. (2) The hydrological process components simulated by the VIC model show that precipitation increases from the upstream to the downstream regions, evapotranspiration is higher in the middle and lower reaches, and the multi-year average values of surface runoff and base flow increase from the upstream to the downstream regions with significant differences, further validating the model's applicability. (3) A comparison of single-model and MMEA simulation results using the EEMD-based (Ensemble Empirical Mode Decomposition) statistical downscaling method reveals that the MMEA matches the observed data the best. Under future SSP2-4.5 and SSP5-8.5 scenarios, the simulation results indicate that hydrological elements change more significantly under the high-radiation and high-emission scenarios (SSP5-8.5), with a particularly noticeable increase in evapotranspiration. [Conclusion] The runoff simulations show that the annual average runoff remains relatively unchanged under the SSP2-4.5 scenario, while it shows a slightly increasing trend under the SSP5-8.5 scenario. Future monthly runoff simulations indicate that most months under the SSP5-8.5 scenario have higher runoff compared to the SSP2-4.5 scenario.