Most of the approaches so far in fabricating core-shell nanoparticles (CSNs) are based on wet-chemical methods. It is usually difficult to achieve highly ordered CSN arrays on substrates from such a wet-chemical method. In this work, highly ordered indium oxide coated indium CSNs, with a structure-dependence photoluminescence, are fabricated on Si substrates using a three-step oxidation process. By controlling the three-step oxidation process, the volume ratio of the oxide shell to the whole CSN can be adjusted continuously from 0 to 1, which results in fine-tuning of the intensity and peak-shift of the photoluminescence from the CSNs. Our work is based on a dry oxidation method for fabricating CSNs, which is capable of achieving highly ordered CSN arrays with tunable nanostructures and optical properties.