With the global climate change and largescale human activities, the runoff and hydrological sequence have changed at watershed scale. Based on daily runoff data from the three hydrological stations of Wuhou Zhen, Yangxian and Ankang in the upper reaches of the Hanjiang River, the inconsistency test was used the Mann-Kendall and Lee-Heghinan method. In addition, the variable hydrological time series of inconsistency was amend based on trend analysis. According to the Pearson-Ⅲ of the frequency distribution curve, the design values under different assure rates were determined to provide guidance for hydraulic engineering design and management. The results showed that annual runoff of the three hydrological stations decreased, and the decline rate from the downstream to the upstream increased. Besides, all of the annual runoff series changed, and the variation time in downstream lags slightly behind the upstream, the catchment was major factor in the controlling downstream flow and mutation. Annual maximum daily runoff had slightly increased at Wuhou Zhen, but showed decreasing trend at Yangxian and Ankang. Corresponding to recent climate and underlying surface conditions, the change of onceinacentury flood design value with consistency correction was greater than history value.