The study on the characteristics of runoff evolution in the basin has a significant meaning to the sustainable development and utilization of the water resources in the river basin and its optimal allocation. In this paper, based on the monthly natural runoff data in Haiyan, Xining and Minhe hydrological stations in Huangshui main stream from 1956 to 2015, inter-annual runoff features, tendency, detection for abrupt changes, and periodicity were analysed by using cumulative anomaly, moving average, Mann-Kendall test and Morlet wavelet analysis method. The results show that the distribution of annual runoff is uneven. The inter-annual runoff fluctuated significantly, experiencing "wet year-dry year-wet year-dry year-wet year" five cycles from 1956 to 2015. On the whole, the runoff of Huangshuiriver showed a rising trend. The flow of the three stations presented linear increase by 0.0011×108m3/a, 0.00247×108m3/a and 0.0120×108m3/a. The principal periods of the stream-flow were 3 years, 9 years and 25 years. The first principal cycle is 25 years while the second and third principal cycles are 9 years and 3 years.