With the impact of climate change and human activities, the consistency of hydrological series is destroyed. Thus, traditional frequency calculation methods are challenged. The variation characteristics of 8 river annual runoff series in the Shiyanghe River Basin were detected using the hydrological alteration diagnosis system, conditional probability distribution and mixed distribu - tion methods were employed to calculate the frequency of annual runoff. The results indicate that the dominant variation type of annual runoff series in Shiyanghe River Basin is a downward jump and the aberrance years are mainly around 1960; the two kinds of distributions of variant series pass the K-S test with all the efficiency coefficients of optimal distributions exceeding 0.97; when design frequency is more than 90%, the design annual runoff of the Dajinghe River and Xiyinghe River derived from the theoretical distribution considering variation has a great difference from that obtained by consistent P-III distribution without regard to variation. Therefore, during the planning design phase of newly-built water projects, the emphasis is analyzing variation features of hydrological data appropriately and selecting rational frequency calculation method for design annual runoff.