We report the evidence that the oxygen defects induced by focusing an intense infrared femtosecond laser pulse in fused silica can be self-organized by the interference pattern between photon and electron plasma wave. Self-organized nanostructure with a sub-wavelength modulation in refractive index exhibits form birefringence which is rewritable and directionally-controllable. Intriguingly, such optical anisotropy, which indicates a remarkable non-reciprocity, has initially evolved from residual birefringence originated from internal stress distribution due to local heating followed by structural change, regardless of interpulse time. This anisotropic light-matter interaction could be interpreted in terms of an asymmetric relation between light polarization and pulse front tilt. Apart from fundamental understanding of self-organization mechanism, the direction of encoded birefringence can introduce an entirely new concept for rewritable optical storage beyond the diffraction limit of light.