Uncertainties in high flows originating from greenhouse gas emissions scenarios, hydrological model structures, and their parameters for the Jinhua River basin, China, were assessed. The baseline (1961–90) and future (2011–40) climates for A1B, A2, and B2 scenarios were downscaled from the general circulation model (GCM) using the Providing Regional Climates for Impacts Studies (PRECIS) regional climate model with a spatial resolution of 50 km × 50 km. Bias-correction methods were applied to the PRECIS-derived temperature and precipitation. The bias-corrected precipitation and temperature were used as inputs for three hydrological models [modèle du Génie Rural à 4 paramètres Journalier (GR4J), Hydrologiska Byråns Vattenbalansavdelning (HBV), and Xinanjiang] to simulate high flows. The parameter uncertainty was considered and quantified in the hydrological model calibration by means of the generalized likelihood uncertainty estimation (GLUE) method for each hydrological model for the three emissions scenarios. It was found that, compared with the high flows in the baseline period, the high flows in the future tended to decrease under scenarios A1B, A2, and B2. The largest uncertainty was observed in HBV, and GR4J had the smallest uncertainty. It was found that the major source of uncertainty in this study was from parameters, followed by the uncertainties from the hydrological model structure, and the emissions scenarios have the smallest uncertainty contribution to high flows in this study.