Due to their tunable properties, silicon nano-crystals (NC) are currently being investigated. Quantum confinement can generally be employed for size-dependent band-gap tuning at dimensions smaller than the Bohr radius (∼5 nm for silicon). At the nano-meter scale, however, increased surface-to-volume ratio makes the surface effects dominant. Specifically, in Si-SiO2 core-shell semiconductor NCs the interfacial transition layer causes peculiar electronic and optical properties, because of the co-existence of intermediate oxidation states of silicon (Sin+, n = 0–4). Due to the presence of the many factors involved, a comprehensive understanding of the optical properties of these NCs has not yet been achieved. In this work, Si-SiO2 NCs with a diameter of 1.1 nm and covered by amorphous oxide shells with thicknesses between 2.5 and 4.75 Å are comprehensively studied, employing density functional theory calculations. It is shown that with increased oxide shell thickness, the low-energy part of the optical transition spectrum of the NC is red shifted and attenuated. Moreover, the absorption coefficient is increased in the high-energy part of the spectrum which corresponds to SiO2 transitions. Structural examinations indicate a larger compressive stress on the central silicon cluster with a thicker oxide shell. Examination of the local density of states reveals the migration of frontier molecular orbitals from the oxide shell into the silicon core with the increase of silica shell thickness. The optical and electrical properties are explained through the analysis of the density of states and the spatial distribution of silicon sub-oxide species.