Turbid/translucent, near colorless (milky) and light blue metamorphic sapphires from Sri Lanka were investigated by the characteristics of their micro/nano inclusions. Heat treatment under N2 environment at 1650 °C was applied to enhance the stones’color and clarity. Such treatment transformed milky sapphires into light-blue ones while turning the already light-blue ones intensely blue. Both sapphire groups exhibited better clarity after the heat treatment. It was found that the development of color especially at inclusion zoning regions is attributed by the inclusions dissolutions. Micro/nano inclusions, such as, rutile (TiO2), ilmenite (FeTiO3) and hematite (Fe2O3), were dissolved by the heat treatment which resulted in blue coloration by the mechanism of Fe2+/Ti4+ charge transfer. The microstructures become different because the dissolution of apatite (Ca5 (PO4)3(OH,F,Cl)) in alumino silicates (Al2SiO5) occurred, resulting in morphological change with the appearance of (Ca, Mg, Al) silicate on the surface. Both natural and heat-treated sapphires showed the rhombohedral crystal structure of Al2O3; however, that the selected area electron diffraction of the heat-treated samples showed finer structure than those of the natural/unheated ones. It demonstrated that the crystalline structure of sapphire was rearranged by the heat-treatment, resulting in improving sapphire’s color and quality.