Owing to the effects of human activities and climate change, the natural hydrological series lost their consistency. In order to adapt to a changing environment demanding for irrigation and water supply engineering design, typical disaggregation method for inconsistent annual runoff process design was proposed. Firstly, the hydrological variation diagnosis system (HVDS)was used to analyze the variation of the annual average flow series and their annual distribution features. Secondly, according to the variation point, annual average flow series was divided into several time periods. Thirdly, the frequency distributions of annual average flow series before and after the change-point were conducted based on the hydrological frequency calculation theory for inconsistent series (HFCT) and the difference of means and various frequency characteristic values were analyzed. Finally, typical disaggregation model was used to calculate the annual runoff process in each time period. This study was applied at the Heyuan Station of Dongjiang River, and the inconsistent annual runoff process was designed. The difference of designed annual runoff process before and after the change-point at the Heyuan Station was analyzed.