The invention discloses a method and a system for repairing flat panel display module Mura defects. The method comprises steps: S1) a standard brightness matrix S for a 255 gray-scale all-white image is acquired; S2) an n gray-scale image is inputted to obtain a flat panel display module, and a display picture of the flat panel display module is acquired to obtain a display picture brightness matrix I; S3) according to the standard brightness matrix S and the display picture brightness matrix I, a brightness normalization factor K is calculated, and the brightness normalization factor K and the standard brightness matrix S are multiplied to obtain a brightness correction matrix T; and S4) according to the difference between the display picture brightness matrix I and the brightness correction matrix T, a compensation data matrix R is obtained. Through building the standard brightness matrix, influences on the repairing result by distortion brought by an imaging brightness sensor and an Mura defect area brightness value can be avoided; and an iterative method is used for Mura defect repairing, and the problem that one-time repairing can not achieve ideal effects can be solved.