A method of controlling a picture quality of a flat panel display for automatically analyzing a shape, a size, and brightness of a display stain of indeterminate shape having an irregular pattern, and compensating brightness of the display stain of indeterminate shape on the basis of the analyzed result is disclosed. The method of controlling a picture quality of the flat panel display comprises measuring brightness of a display stain, which is generated on a flat display panel, at a vertical direction and a horizontal direction, respectively; imaginarily dividing the display stain in a predetermined distance along a direction that a brightness change is large among the vertical direction and the horizontal direction in accordance with the measured result; detecting edge points where divided border lines of the divided display stains and an edge of the display stain are joined; determining compensation values, which are applied to a plurality of compensation applying surfaces that are defined by the edge points and the divided border lines within the display stain; and adjusting digital video data to be displayed at the compensation applying surfaces using the compensation values.