The relevant statistical properties including trends, periodicities, dependences, persistence and the consistent of low and high runoff of annual runoff for the main rivers in the upper reaches of Yangtze River, are discussed based on the stochastic analysis, wavelet analysis and set pair analysis. The results show that the annual runoff sequences in main rivers have outstanding treads, the different periodicities and the positive persistence structure, the periodicities are unequal in time, the auto correlation and cross correlation between the annual runoff sequences exist, and the spatial distribution of low runoff and high runoff is consistent.