Photo-thermo-refractive (PTR) glass doped with rare-earth ions has attracted considerable attention due to its excellent linear photosensitivity and laser performance. This study investigates the nonlinear photosensitive nanocrystallization induced by ultrafast laser irradiation in Nd-doped PTR glass. Phase contrast microscopy reveals that both Gaussian and Gaussian-Bessel beams can modulate the refractive index positively or negatively, depending on specific conditions. Notably, Gaussian-Bessel beams can significantly extend the thickness of the laser-modified layer. Optical spectra indicate the formation of silver nanoparticles, with concentration increasing as pulse energy increases. Furthermore, X-ray diffraction and transmission electron microscopy confirm the precipitation of nanocrystals with the composition of NaF following laser irradiation and thermal treatment, consistent with conventional PTR glass. The nonlinear optical characteristics of the treated sample are evaluated and successfully applied in a passive Q-switched laser, exhibiting both gain characteristics and saturable absorption. This study provides an effective strategy for multifunctional integrated on-chip devices that possess high damage thresholds and enhanced stability.