Oxide glass is an industrial material with advantages such as optical transparency and shaping ability of the melt, but at the same time, it is a bad conductor of heat due to its disordered structures. Therefore, heat dissipation in glass components often becomes a problem and its applications to the thermal management has been limited to use as a heat insulator. To break this mold and to apply it to fields, e.g., transparent sealing materials, for which low thermal conductive glasses and organic polymers have been conventionally used, we fabricated an MgO-dispersed glass-ceramics in our previous work. It comprises MgO crystal and glass matrix and their reflective indices are matched, leading to optical transparency and improvement in thermal conductivity. Here we investigate the atomic-scale structures in the MgO-dispersed glass-ceramics by nuclear magnetic resonance, etc. and attempt to further improve the thermal conductivity and the transparency. As a result, we show an MgO-dispersed glass-ceramic with a thermal conductivity of 3.3 W (m-1 K-1), corresponding to 300% of that of the glass matrix, high optical transparency, and glass transition. This report highlights that our strategies pave the way for development of novel transparent, functional glass-ceramics.