Understanding the phase transformation in glass and the morphology of related nanostructure after femtosecond laser irradiation is of great importance for fabricating functional optics, in which glass crystallization is involved to obtain nonlinear optical properties. We report on the crystallization inside lithium niobium silicate glass induced by fs laser irradiation. Energy-dispersive X-ray spectroscopy coupled to scanning transmission electron microscopy (STEM/EDS) and transmission electron microscopy confirm a nanoscale phase separation whereby LiNbO3 crystals are embedded in lamella-shaped frames of amorphous SiO2. The obtained nanostructure may have applications in fabricating second-order nonlinear optical devices.