Carbon nanotubes (CNTs) have demonstrated superior mechanical, electrical, and thermal properties. Our previous studies have shown that the Heli-coil CNTs (HCNTs) perform better than the straight CNTs as nanoscale reinforcements, primarily due to their heli-coil structural configurations that can additionally provide mechanical-interlocking-mechanisms between the microfibers and resin. Pristine CNTs are inert and do not disperse well in polymers and form weak bonds with resin molecules. One of the techniques to improve the dispersion of CNTs and their bonding effectiveness is to chemically functionalize them. In this research, HCNTs that were covalently functionalized using a mixture of nitric, sulfuric, and hydrochloric acids following 16 different procedures, varying the process parameters (i.e., sonication time, acid molarity, and mixing sequence) were used. The pristine and functionalized HCNTs (FHCNTs) were incorporated into epoxy resin at very low weight percentages (i.e., 0.02, 0.04, and 0.06 wt%), processed, used to fabricate nanocomposite test specimens, and then tested according to ASTM standards. The main objective of this research was to investigate the effects of chemical functionalization process parameters and wt% of FHCNTs on the mechanical performance of polymeric nanocomposites. The test results showed improvements of up to 5.7%, 35.1%, 11.1%, 49.5%, and 60% for the tensile strength, fracture toughness, modulus, strain-to-failure, and hardness, respectively, that were mostly related to 0.02 wt% of FHCNTs reinforcements for the functionalization procedures 2, 4, and 10. Additionally, the fractured specimens were inspected and analyzed using 3D scanning-laser-confocal-microscopy and SEM imaging, and the most effective functionalization processes were recommended for structural nanocomposite applications.