Silver-doped silicate composite glass had been synthesized with an ion-exchanged method. Grazing incidence small angle X-ray scattering (GISAXS) technique was used to investigate the size and distribution evolutions of Ag nanoparticles in the glass matrix in a subsequent thermal treatment process. GISAXS experiment reveals a change of size distribution of Ag nanoparticles from bimodal distribution to one-size distribution in annealing at 300 °C. The results demonstrate that the normalized volume fraction of smaller particles with average diameter of 6.4 nm almost no changed, but the bigger metastable ones dissolved gradually in an exponential decay way during the annealing process. It can be concluded that a multilayer nanostructure composed of silver nanoparticles was formed in the thermal process.