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In recent years, the impacts of climate change and human activities generate the change of hydrological conditions, leading that the hydrological frequency calculation data don't satisfy the premise of consistency. For the hydrological frequency calculation about inconsistency series, this paper proposed the inconsistency of hydrological frequency calculation method called TFPW-MK-Pettitt and EEMD. First, texting the hydrological series inconsistency used trend-off pre-whitening Mann Kendall-Pettitt methods; Second, the EEMD method was applied to revise uniformity hydrological series; Finally, calculating the hydrological frequency of correcting series. The following conclusions 1) the TFPW-MK-Pettitt method is suitable for our country hydrological series by statistical experiment; 2) the year of 1956 to 2012, runoff series of the Yichang station have downward trend by using the proposed method; 3) the design value of frequency calculation results is smaller 10% than before correction by using the EEMD method.