Silica glass pairs were directly bonded by wet chemical surface activation at a low temperature. A smooth joint interface with no voids and micro cracks was obtained with the assistance of a 250 °C heat treatment and a pressure of ∼30 MPa, and the excellent transmittance of the bonded pair was demonstrated by UV-Vis absorptions. This new method can tolerate a silica glass surface roughness as high as 6 nm. A demo chip with a microfluidic channel was also prepared by this method. A modified model for the glass-to-glass bonding mechanism is proposed based on the surface and interface characterization. Raman scattering analysis showed that Si–O–Si linkages at the silica glass surface were broken, and colloid-like hydrolyzed layers formed on the glass surface after the activation treatment. TEM and EELS results revealed that the 3D glass structure of the Si–O–Si linkages formed again at the interface of the directly bonded silica glass pairs after low-temperature annealing.