Carbon-based nanoparticles (CBNs) are regarded as promising nanofillers in nanocomposites to produce high-performance fiber-reinforced polymers (FRPs). To date, no systematic investigations have been carried out on the structural variations of nanofillers and their influences on dispersion characteristics, which give nanocomposites their mechanical and durability properties. Moreover, environmentally unfriendly organic solvents are used to exfoliate and disperse CBNs in a polymer matrix. This study developed a green, easy approach to preparing epoxy/CBN nanocomposites. We demonstrated graphene oxide’s (GO) effective dispersion capacity, creating good interface interaction that dramatically influenced properties at loadings as low as 0.4 wt%. The tensile strength and toughness of the epoxy increased by about 49%; and 160%, respectively. Incorporating 0.4 wt% of multi-wall carbon nanotubes (MWCNTs), graphene nanoplates (GNPs), or GO into the epoxy increased the modulus storage by around 17%, 25%, and 31%, respectively. Fractography analysis of fracture surfaces indicated the primary reinforcing mechanisms (crack deflection and penning) as well as the secondary mechanism (bridging effect) enhancing the mechanical characteristics of nanocomposites. Incorporating GNPs, GO, or MWCNTs into the epoxy decreased the water absorption at saturation by about 26%, 22%, and 16%, respectively.