The invention discloses a research method for influence on medium and long term runoff forecasting by south branch troughs. The research method includes the steps that according to definition of the winter and spring south branch troughs, the intensity index of the winter south branch trough and the intensity index of the spring south branch trough are calculated; the intensity indexes obtained through calculation are standardized, and interannual variation characteristics of the south branch troughs are obtained through analysis; the strong and weak critical values of the south branch trough intensity index are defined, and then strong and weak years of the winter south branch trough and the strong and weak years of the spring south branch trough are respectively screened out; the rainfall condition in the strong south branch trough year is compared with that in the weak south branch trough year in the South; correlation analysis is carried out on the intensity index of the winter south branch trough, the intensity index of the spring south branch trough and actual rainfall data of a hydrometric station in the South to obtain the south branch trough coefficient and correlation coefficients thereof with actual rainfall in different months, the large correlation coefficient serves as the correlation coefficient of the south branch troughs to runoff of all hydrometric stations in the South and serves as a forecast reference of medium and long term natural runoff, and therefore forecast accuracy is improved.