Studying the impact of climate variability is important for the rational utilization of water resources, especially in the case of intensified global climate variability. Climate variability can be caused by natural climate variability or human-caused climate variability. The analysis of Jinghe River Basin (JRB) may not be comprehensive because few studies have concentrated on natural climate variability. Therefore, the primary goal is to explore the impact of natural climate variability on runoff. A modified Mann–Kendall test method was adopted to analyze the aberrance point to determine the natural condition period during which runoff was only influenced by natural climate variability. Then, the Monte Carlo method was employed to extract segments of monthly runoff in the natural condition period and combine them to construct a long series to reduce the instability. Results indicate that the percentage of runoff variability affected by natural climate variability is 30.52% at a confidence level of 95%. Next, a topography-based hydrological model and climate elasticity method were used to simulate runoff after the aberrance point without considering the impact caused by local interference. Through a comparison of the measured and simulated runoff, we discovered that local interference has the greatest impact on runoff in the JRB.