Global water resources are affected by climate change as never before. However, it is still unclear how water resources in high latitudes respond to climate change. In this study, the water resource data for 2021–2050 in the Naoli River Basin, a high-latitude basin in China, are calculated by using the SWAT-Modflow Model and future climate scenarios RCP4.5 and RCP8.5. The results show a decreasing trend. When compared to the present, future streamflow is predicted to decrease by 2.73 × 108 m3 in 2021–2035 and by 1.51 × 108 m3 in 2036–2050 in the RCP4.5 scenario, and by 8.16 × 108 m3 in 2021–2035 and by 0.56 × 108 m3 in 2036–2050 in the RCP8.5 scenario, respectively. Similarly, groundwater recharge is expected to decrease by −1.79 × 108 m3 in 2021–2035 and −0.75 × 108 m3 in 2036–2050 in the RCP 4.5 scenario, and by −0.62 × 108 m3 in 2021–2035 and −0.12 × 108m3 in 2036–2050 in the RCP 8.5 scenario, respectively. The worst impact of climate change on water resources in the basin could be frequent occurrences of extremely wet and dry conditions. In the RCP 4.5 scenario, the largest annual streamflow is predicted to be almost 14 times that of the smallest one, while it is 18 times for the groundwater recharge. Meanwhile, in the RCP 8.5 scenario, inter-annual fluctuations are expected to be more severe. The difference is 17 times between the largest annual streamflow and the lowest annual one. Moreover, the value is 19 times between the largest and lowest groundwater recharge. This indicates a significant increase in conflict between water use and supply.