In this study, feather was used as the source of protein and combined with copper and boron salts to prepare wood preservatives with nano-hydroxyapatite or nano-graphene oxide as nano-carriers. The treatability of preservative formulations, the changes of chemical structure, micromorphology, crystallinity, thermal properties and chemical composition of wood cell walls during the impregnation and decay experiment were investigated by retention rate of the preservative, Fourier transform infrared spectroscopy (FT-IR), scanning electronic microscopy-energy dispersive spectrometer (SEM-EDS), X-ray diffraction (XRD), thermoanalysis (TG), and confocal Raman microscopy (CRM) techniques. Results revealed that the preservatives (particularly with nano-carrier) successfully penetrated wood blocks, verifying the enhanced effectiveness of protein-based preservative with nano-carrier formulations. Decay experiment demonstrated that the protein-based wood preservative can remarkably improve the decay resistance of the treated wood samples, and it is an effective, environmentally friendly wood preservative. Further analysis of these three preservative groups confirmed the excellent function of nano-hydroxyapatite as a nano-carrier, which can promote the chelation of preservatives with higher content of effective preservatives.