To analyze the mutation and periodical variation of runoff and sediment load more effectively, the existing methods are summarized and then a detailed comparison is carried on. The experiment data used comes from the Datong Station and Yichang Station of Yangtze River. By comparing the principle, result and applicability of each method, it is concluded that the sequential cluster method is most suitable for mutation analysis with both simple calculation and accurate result, while the wavelet analysis method is highly developed and recommended for periodical variation analysis.