During recent decades, hydrological regimes at the three outlets (i.e., Songzi, Taiping and Ouchi outlets) of Lake Dongting have been greatly changed, which is comprehensively caused by the cutoff works in the Jingjiang River channels, operation of the Gezhou Reservoir, flood storage and operation of the Three Gorges Reservoir (TGR), and soil-water conservation practices in the upper reaches of the Yangtze River Basin. The obviously hydrological variability in the basin would inevitably influence the flood disasters control, water resources management, and protection of water ecology and environment. For investigating the changes and variability in the hydrological process occurred in the basin, in this study we employed the hydrological variability detection system (composed of namely primary diagnosis, detailed diagnosis and comprehensive diagnosis) and the Zivot-Andrews unit root test method, mainly to identify the changes in the annual maximum peak flood series and annual highest flood level series measured at five stations at the three outlets of Lake Dongting, as well as attributing their physical causes. The diagnosis system includes many methods, by which shortages of a certain method can be overcome and different results of methods can be compared. The Zivot-Andrews unit root test can be used to determine the local trends in a hydrological series. Diagnosis results indicate that the annual maximum peak flood processes at the three outlets consistently show a similar downward trend, which is closely related to the changes in the water-sediment diversion ability and upstream flow changes. A downward jump point in 1968 was detected at some stations, and the three outlets cut-off construction can be the reasons. The annual maximum peak flood process at the Kangjiagang station has local trends, and the trend slope was greatly changed before and after the local trend year 1968. It can be caused by the influence of the three outlets cut-off construction. The annual highest flooding water level series presented a downward jump in 2004, mainly due to the erosion of flood channels, peak flow reduction, jacking function weakened and the increases in the upstream and downstream changes.