This invention relates to a method and a system for writing fiber Bragg gratings (FBG) having apodized spectrum ("apodized FBG") on optical fibers. An amplitude modulation mask is placed between a focusing cylindrical lens and the optical fiber. By reducing the distance between the amplitude mask and the fiber, the present invention can minimize diffraction effects that may be induced by long propagation distance of a laser beam passing through a small and/or narrow aperture in the amplitude mask. The method and system of the present invention can be applied to write FBG with apodized spectrum with small amplitude mask to achieve full width at half maximum (FWHM) bandwidth (BW) wider than 1.2 nm and to achieve side lobe suppression ratio (SLSR) as high as 30 dB. These method and system generally increase the laser power efficiency of the laser used in FBG inscription and optimizes the grating index modulation profile.