[Objective] Studying the nonlinear variations of runoff in Yihe River and the climate factors in different time scales, which was expected to provide theoretical basis for analizing the impact of climate change on runoff. [Methods] The methods of ensemble empirical mode decomposition(EEMD), Mann-Kendall test, Pearson correlation analysis and Linear regression were adopted. [Results] The runoff appeared a significant linear downward trend(p<0.01) during 1951-2013, with a rate of 3.33×10⁸ m³/10 a butan aberrant trend existed around 1976. Meanwhile, runoff was decomposed into four IMFs. The contribution of variance of inter-annual scale(quasi-3 and quasi-6-year) to the overall one was the largest, reaching 58%. The contributions of inter-decadal scale(quasi-13-year) and multi-decadal scale(quasi-31-year) were 11% and 6%, respectively. Subsequently, the contribution of nonlinear variation to the overall runoff was 25%. [Conclusion] The effects of climate factors(PDO, ENSO, temperature and precipitation) in different time-scales on runoff and its mechanism were proved different. The climate factors in inter-decadal scale and multi-decadal scale are more closely related to runoff change.