Current manufacturing challenges arising from poor-dispersion and high-viscosity significantly hinder the realization of potentials that high-performance multifunctional multiscale composites contain. Especially in fiber-reinforced composite systems, large intermolecular aggregates formed by Van der Waals forces of carbon nanotubes (CNTs) can cause a filtration phenomenon in porous media, which challenges the conventional vacuum-assisted resin transfer molding (VARTM) process. This paper discusses the development of a functionalized-carbon nanotube (CNT)/fiber-reinforced polymer composite material. Chemical functionalization was performed via oxidization. Oxygen-containing function groups were found in subsequent oxidized multi-walled carbon nanotubes (MWNTs), providing greater reactivity of oxygen-containing groups with EPON862/EPI-W than pristine CNTs. This reaction can create the potential to take full-advantage of the extraordinary properties of CNTs. A novel vacuum-assisted infusion setup was also applied to incorporate CNTs to enhance the interlaminar length and modulus of composite materials. The enhancement of mechanical properties was remarkable for functionalized multiscale composites when compared with pristine CNT-reinforced composites. Tensile-strength increased by 15.8% and tensile modulus increased by 27.2%. Moreover, both the shear strength and short-beam modulus increased by 6% and 11.8%, respectively, demonstrating improved interlaminar properties. The strain-stress curves also exhibited an increase in toughness. Corresponding SEM data verified improved interfacial interactions. CNTs became one part of the cross-linked structure instead of separate fillers in this hybrid material system. FTIR, RAMAN, DSC and DMA were used to investigate the influence of functionalization. Coefficient of thermal expansion (CTE) and electrical conductivity of the multiscale composites were also tested.