To carry out frequency analysis for the Manas River in Xinjiang based on the nearly 60 years runoff sequence, a mixed distribution model and a conditional probability distribution model were constructed using the Mann-Kendall test and t-test. The results shows that the annual runoff series of the Manas River in 1956~2014 have great variations and the year 1995 is the sequence variation year. In the upper part of the fitted curve, the mixed distribution and the conditional probability distribution are similar, but big difference exists compared the P-III distribution. In the middle of the fitted curve, the fitting effect of the mixed distribution is better than both conditional probability distribution and P-III distribution. In the lower part of the fitted curve, the fitting effects of all the three distributions are pretty good, and there is no obvious fluctuations. Through the K-S test analysis and comparing the values of OLS, ABS and AIC, the mixed distribution model is more suitable for frequency analysis of the annual runoff in the Manas River Basin.