The present invention discloses a method and system for selecting an image region that facilitates blur kernel estimation, in which the method includes: calculating a relative total variation value of each pixel in a blurred image to obtain a relative total variation mapping image; setting a threshold value to determine whether respective pixel in the image is a boundary pixel or not; then sampling the blurred image and its relative total variation mapping image to obtain a series of image patches; and finally counting the number of boundary pixels in each mapping image patch and selecting out an image region that facilitates blur kernel estimation. According to the method and the system, the problems of excessive dependency on operator experience, low efficiency and the like in the existing region selection methods are effectively solved. The image region that facilitates blur kernel estimation is automatically selected out. And the method and the system are suitable for the application occasion of the blur kernel estimation in an image deblurring algorithm.