The structure of initial glasses in the Na2O–K2O–Nb2O5–SiO2 system with an Nb2O5 content ranging from 5 to 39 mol % and their structural transformations in the course of isothermal treatments at different temperatures are investigated using small-angle X-ray scattering (SAXS) and X-ray powder diffraction. It is demonstrated that, in glasses containing 15 mol % Nb2O5 and more, the metastable phase separation is the primary process responsible for the formation of a microinhomogeneous structure. With further heat treatment of these glasses, NaNbO3 crystals precipitate in regions with a high Nb2O5 content. In this case, each region has a heterogeneous structure and consists of NaNbO3 microcrystals surrounded by layers of the high-silica matrix. These layers hinder transfer processes and, consequently, recrystallization, which ensures the stability of the heterogeneous structure and, correspondingly, constant sizes of microcrystals at temperatures up to 750–800°C. The intensity of light scattering is determined primarily by the sizes of regions formed upon phase separation. A decrease in their size with an increase in the niobium oxide content leads to a decrease in the light scattering loss and an increase in the transparency of heat-treated samples. The interference effects associated with the heterogeneous structure of high-niobate phase regions also favor an increase in the transparency of the prepared materials.