Based on the measured runoff data of the Three Outlets of the South of Jingjiang River from 1956 to 2016, the temporal and spatial variation characteristics of runoff were studied in the base period and change period by trend analysis and wavelet analysis methods, presuming 1989 as the dividing point of water system connectivity variation. The results showed that the decline rates of average annual runoff in the base period and change period were 194.57×106 m3/a and 76.82×106 m3/a, respectively, which showed a downward trend. The runoff was mainly concentrated in the wet season, accounting for 60%-70%. Runoffs in the four hydrological seasons decreased by 40%-80% in the change period, and the decline rate in the dry season was as high as 77%. Runoff changes presented three types of periodic cycles, the number of short-term cycle alternation between wet and dry phases in the change period was about two times more than that in the base period; whereas the range and central value of the long-term cycles were shortened by about six years. The runoff in Xinjiangkou and Guangjiapu hydrological stations were about 2/3 of the total flow of the Three Outlets area, which were concentrated in the west branch of Songzi river and the east branch of Ouchi river. The results can provide a scientific and technical support for the regulation and storage of water resources in the Three Outlets area and the Dongting Lake.