By use of Kendall trend test method, R/S analysis method, run-length analysis method and Markov process analysis method, the paper analyzed the long-term evolution law of annual runoff at the water source of central Yellow River diversion project. The annual runoff timing at Hequ station of the Yellow River showed a significant decreasing trend during the whole period 1978 to 2010. According to the result,the runoff will continue to show a more significant decreasing trend in the future. The occurrence probability of continuous multi-annual high flow state, normal flow state and low flow state decreased with the increase of consecutive years. In the long-term evolution process of high and low state, the reproduce time of partial low flow year is the shortest and the reproduce time of partial high flow year is the longest.The annual runoff at water source of the central Yellow River diversion project will show a more significant decreasing trend in the future; In the process of high and low evolution of annual runoff, it is more likely to appear low flow year. The study can provide a scientific basis for the sustainable development and utilization of water resources on the Yellow River and the regulation of supply and demand of the central Yellow River diversion project.