The present invention provides a method and system for repairing flat panel display, which repairing hot pixels of the flat panel display by femtosecond laser. The flat panel display comprises a LCD module and a color filter disposed on the top of the LCD module, wherein the surface of the color filter corresponding to the LCD module further has a color photoresist layer. The femtosecond laser is projected onto the color photoresist layer corresponding to the hot pixels such that a phenomenon of nonlinear multiple photons absorption can be occurred to change property of the color photoresist layer so as to transform the hot pixels into dead pixels.