The invention discloses a sub-season-season-interannual scale integrated climate mode set prediction system. The system comprises an initialization module, a high-resolution climate mode module, a set prediction module and a prediction post-processing module. The initialization module is used for downloading, extracting and processing multi-source data including atmosphere, land surface, ocean and sea ice, and using external parameters for controlling and achieving preprocessing such as data selection, checking and horizontal and vertical interpolation of meteorological elements, and the initialization module is suitable for data preprocessing of operation in all climate modes. The high-resolution climate mode module is used for carrying out objective quantitative prediction on multi-circle coupling collaborative change of atmosphere, land surface, ocean and sea ice; the set prediction module is used for generating any number of set prediction sample members combined by physical parameter tendency random disturbance and an initial value time lag method. The invention provides the climate prediction with high resolution, high prediction accuracy and good controllability, and provides multi-time-scale and multi-space-scale climate prediction of atmosphere, land surface, ocean and sea ice.