The invention discloses an SAR image segmentation system and a segmentation method based on immune clone and projection pursuit. The system comprises an image characteristic-extracting module, an initial label-selecting submodule, a projection direction-selecting submodule and a subspace clustering submodule, wherein the image characteristic-extracting module extracts the gray co-occurrence matrix characteristics, the wavelet characteristics, the brushlet characteristics and the contourlet characteristics of an input image; the initial label-selecting submodule clusters the image characteristics to acquire and transmit an initial label to the projection direction-selecting submodule for calculating a linear judgment analysis projection index and acquiring an optimal projection direction; the subspace clustering submodule projects the image characteristics in the optimal projection direction, acquires and clusters an optimal subspace to acquire a clustering label, returns the clustering label to the initial label-selecting submodule for iteration, acquires a final clustering label corresponding to image pixels and acquires a final image segmentation result. The invention has the advantage of high segmentation accuracy and can be applied to civil and industrial fields or as martial reconnaissance means.