Understanding the responses of the hydrological cycle and extreme events to climate change is essential for basin water security. This study systematically assessed climate change impacts on runoff and floods in the Fujiang River basin, which is the main tributary of the upper Yangtze River, China, using the Soil Water Assessment Tool (SWAT) driven by the latest climate simulation of 14 General Circulation Models (GCMs) under two Shared Socioeconomic Pathways (SSP2-4.5 and SSP5-8.5). This study indicates a generally warmer and wetter climate projected in the Fujiang River basin, and correspondingly an overall increase in projected ensemble annual mean runoff, monthly runoff, monthly high flow (Q05), and monthly low flow (Q95) in the periods of 2021–2060 and 2061–2100, with the long-term period being more substantial than that of the near future, especially for SSP5-8.5. However, the projected changes in monthly runoff show a large spread across GCMs, with greater increases mainly occurring in the early rainy season. Most of the GCMs show that projections of Q95 will substantially increase compared to Q05. The intensity and frequency of floods with a 30-year return period are likely to increase, especially under SSP5-8.5. Despite the uncertainties in projected future changes in runoff, these findings highlight the complexity of runoff response to climate change, promoting the need for adaptive water resource management.