We present an original study on the non-destructive evaluation of the microstructure evolution of fused silica induced by pulsed UV laser irradiation at low fluence (less than 50% Fth). Positron annihilation spectroscopy discloses that the spatial size of the vacancy cluster is increased exponentially with the linearly elevated laser fluence. Particularly, the vacancy cluster size in bulk silica is significantly increased by 14.5% after irradiated by pulsed 355nm laser at F=14J/cm2 (50% Fth), while the void size varies only ∼2%. UV laser-excited Raman results suggest that the bond length and average bond angle of SiOSi bridging bond are both slightly reduced. Results reveals that the rearrangement process of (SiO)n fold rings and breakage of the SiO bridging bond in bulk silica occurred during pulsed UV laser irradiation. The micro-structural changes were taken together to clarify the effect of sub-threshold laser fluence on material stability of silica glass. The obtained data provide important information for studying material stability and controlling the lifetime of fused silica optics for high power laser system.