A novel preparation process is developed to effectively disperse biomass nanofibers such as cellulose, chitin, and chitosan nanofibers, in a hydrophobic bisphenol-A-type epoxy resin. The nanofibers (NFs) are incorporated into an amphiphilic epoxy resin and then mixed with the diglycidyl ether of bisphenol A. The mechanical properties of the epoxy resin improved by 27-39%. Differences in reinforcement properties based on the NF type are discussed in terms of aspect ratio, dispersibility, and interfacial adhesion with the epoxy matrix. Chitin nanofibers (ChNFs), which have the highest aspect ratio and relatively high hydrophobicity, show the strongest reinforcement because of their dense NF network and superior interfacial adhesion to the epoxy matrix. NF dispersion improved both tensile strength and elongation at break, making the NF/epoxy composites tougher than the neat epoxy resin, while increasing the impact and adhesive strength. The NF network structure has a low coefficient of thermal expansion (CTE) that restricts the molecular motion of epoxy chains, leading to lower CTE and higher glass transition temperatures than that of the neat epoxy resin. A wet-rotating disc milling (WRDM) process further improved NF dispersibility in the matrix, increasing the tensile strength and elongation at break of the WRDM-treated ChNF/epoxy composite by 48 and 71%, respectively, compared to that of the neat resin. This method successfully dispersed biomass NFs in a hydrophobic bisphenol A-type epoxy resin, enhancing its mechanical and thermal properties while addressing drawbacks of the epoxy resin such as brittleness, thermal expansion, and cure shrinkage.