We evaluated the impact of climate change on the runoff of the Xin'anjiang-Fuchunjiang hydropower station basin, put forward the adaptive scheduling scheme under different climate change scenarios, and analyzed the uncertainty. The results show that, during 2016-2099, the runoff of Xin'anjiang Reservoir Basin will decrease by 5.4%-5.8%, and the runoff of the Jinhua River Basin and Qujiang River Basin will increase by 6.2%-7.5% and less than 0.8%, respectively. Under the adaptive scheduling mode, the total generating capacity of the Xin'anjiang-Fuchunjiang hydropower station is expected to increase by 3.43%-3.85% compared with the conventional dispatching. The maximum discharge of the Xin'anjiang and Fuchunjiang hydropower stations will decrease by 22.74%-33.29% and 16.57%-17.63%, respectively. The total abandoned water of the two hydropower stations will decrease by 81.61%-99.99% and 52.98%-58.64%, respectively. In addition, the scheduling mode adapts well to the radiation intensity and the uncertainty among different GCMs.