[Obejective] The variation of runoff in the Tuotuo River in the headwaters of the Yangtze River in the past 51 years under different time scales of precipitation, such as interannual, interdecadal and season, and also the lagging effect of runoff on precipitation were analyzed in order to provide a theoretical basis for the management and utilization of water resources in the basin.[Methods] This paper used the runoff and precipitation data of hydrological station and the meteorological station in Tuotuo River of the Yangtze River source region from 1961 to 2011, and combined the statistical methods such as cumulative anomaly, variation coefficient, concentration frequency and concentration period, to investigate the variations of runoff and precipitation at decadal, annual and seasonal time scales. The hysteresis effect of runoff to precipitation was also discussed.[Results] The annual and seasonal runoff of the Tuotuo River Basin in the past 51 years showed an increasing trend. The annual, spring and summer runoff increased significantly. The climatic tendency rates were 1.00×10⁸ m³/10 a, 6.00×10⁶ m³/10 a, 6.30×10⁷ m³/10 a, respectively. The runoff of the river was mainly concentrated in the period from May to October, especially from late July to mid-August. There was a significant correlation between runoff and precipitation. The runoff had a lagging effect on precipitation in most years, and the average lag time was about 10 d. The hysteresis period was observed being increased over the past time.[Conclusion] In the past 51 years, the trend of runoff and precipitation in the study area had increased, and the lag effect of runoff on precipitation was about 10 days.