The change in natural runoff is highly relevant to total river flow dispatch and water resource utilization in the Yellow River Basin (YRB). Based on the annual mean temperature and total precipitation records from 70 meteorological stations from 1961–2020, the impact of climate change on the natural runoff of the YRB is investigated using the Mann-Kendall (M-K) test and Bivariate Wavelet analysis methods. Results show that the annual mean temperature over the YRB increased by 0.33 °C decade⁻¹ during 1961–2020, with a warming rate of more than 0.40 °C decade⁻¹ observed in its northern part. The annual total precipitation increases by 10–20 mm decade⁻¹ in the northwest YRB, while it decreases by 20–30 mm decade⁻¹ in the southeast YRB. The result of the M-K test shows abrupt variations in temperature and natural runoff, especially in the 1980s and 1990s. The decrease in natural runoff is closely tied to the increase (decrease) in temperature (precipitation), especially for the period 1993–2020. The bivariate wavelet coherence analysis further suggests that the decrease in the natural runoff, which has persisted over the past 60 years, is primarily driven by precipitation reduction rather than regional warming. In the stage of rapid warming, the inter-decadal influence of precipitation on natural runoff gradually changes to the influence of inter-annual fluctuation. The finding contributes to providing an important scientific basis for evaluating the optimal allocation of water resources in arid and semi-arid areas against the background of climate change.