In the current paper, we report the results of surface modification of cubic Y2O3 films employing carbon-ion implantation. The characterization results demonstrate the formation of a stable yttrium oxalate-based structure with cavities filled with carbon clusters. Theoretical simulations demonstrate that the incorporation of eighteen-atom carbon clusters into the cavities of Y2(C2O4)3 does not lead to valuable changes in the crystal structure of yttrium oxalate. X-ray diffraction and optical measurements demonstrate that the subsurface bulk area of cubic yttrium oxide remains unperturbed. The oxalate “skin” thickness with embedded carbon clusters is estimated to be approximately 10 nm. The prospective employing the method to manage optical properties and increase the biocompatibility of yttria and lanthanide oxides are discussed.