Abstract: A linear regression analysis method, mutation test method, etc. were used to analyze the trend and abrupt changes of climate factors such as the average annual temperature, annual precipitation, and annual evaporation in the Bosten Lake Basin from 1980 to 2018 and their impact on the runoff of the Kaidu River. Results show that from 1980 to 2018, the annual average temperature in the Bosten Lake Basin showed a fluctuating upward trend, the rate of change is 0.15°C (10 a)⁻¹, and the annual precipitation increases at a rate of 0.765 mm (10 a)⁻¹. However, the annual evaporation appears to gradually decrease at a rate of −11.6 mm (10 a)⁻¹, and the climate of the basin has a trend from dry to wet. The response of the Kaidu River’s runoff to sudden changes in climate factors shows that the Kaidu River’s runoff from 1980 to 2018 has a significant increase at the level of 0.05. Research on the impact of the basin due to climate change on the runoff of the Kaidu River has shown that the annual average temperature of the basin has the greatest correlation with the runoff of the Kaidu River with a correlation coefficient of 0.463. Moreover, there is a small correlation between the annual precipitation, annual evaporation, and runoff with correlation coefficients of 0.276 and −0.03, respectively. A comparative analysis found that the impact of climate change in the Bosten Lake Basin on the runoff of the Kaidu River in descending order is annual average temperature>annual precipitation>annual evaporation.