Taking the Hanjiang River basin located in eastern Guangdong and southwest Fujian as the research object, the spatial pattern of land use in the basin in 2050 was predicted based on CA-Markov model. The SWAT distributed hydrological model was constructed, and the hydrological simulation was carried out with the future land use scenario and climate change scenario as variables to analyze the temporal and spatial evolution characteristics of ecological flow of Hanjiang River under different scenarios. The results show that the future urbanization expansion will make the middle and upper reaches of the Meijiang River become the most sensitive area of ecological flow to land use change in the Hanjiang River Basin. Land use and climate change will lead to the overall decrease of flow in dry season of the Hanjiang River Basin, and the flow in dry season is more sensitive to environmental change. The change characteristics of ecological flow in the Hanjiang River Basin will show a downward trend from southwest to northeast, and the ecological flow in the middle and upper reaches of Meijiang River will be improved. The regional ecological flow in the upper reaches of Meijiang River and Tingjiang River is more sensitive to climate change. The total runoff of the Hanjiang River Basin decreases, but the differentiation of flow in dry season and wet season intensifies. In the long run, the risk of ecological flow guarantee in dry season may further increase.