Electrical conductivity and mechanical properties of PA6/carbon nanofillers nanocomposites are highly dependent on the formation of PA6 transcrystalline layers onto the carbon nanofillers. In the current study, the substantial effects of PA6 viscosity and CNTs modification on transcrystalline layer formation in nanocomposites were investigated both experimentally and theoretically. FESEM, TEM, and solvent extraction observations showed almost identical morphological features for all samples, with well-dispersed carbon nanofillers within the matrix, and dispersed droplets morphology. Therefore, the differences in electrical conductivity among various nanocomposites were attributed to the only variable, which was differences in PA6 transcrystalline layer formation. It was found that employing high viscosity PA6, as well as modifying CNTs, both result in reduced transcrystalline layer formation and thus higher electrical conductivity, as corroborated by the theoretical modeling. Moreover, the evaluation of mechanical properties further elucidated that the transcrystalline layer formation can improve the tensile strength, Young’s modulus, and heat deflection temperature. Hence, on the one hand, transcrystalline layer formation endowed nanocomposites with superior mechanical properties due to the strong interfacial adhesion between the nanofillers and polymer matrix. On the other hand, however, it decreased the electrical conductivity by hindering electron tunneling through the dense and insulative transcrystalline layers.