The outstanding properties of carbon nanotubes (CNTs) present some limitations when introduced into rubber matrices, especially when these nano-particles are applied in high-performance tire tread compounds. Their tendency to agglomerate into bundles due to van der Waals interactions, the strong influence of CNT on the vulcanization process, and the adsorptive nature of filler–rubber interactions contribute to increase the energy dissipation phenomena on rubber–CNT compounds. Consequently, their expected performance in terms of rolling resistance is limited. To overcome these three important issues, the CNT have been surface-modified with oxygen-bearing groups and sulfur, resulting in an improvement in the key properties of these rubber compounds for their use in tire tread applications. A deep characterization of these new materials using functionalized CNT as filler was carried out by using a combination of mechanical, equilibrium swelling and low-field NMR experiments. The outcome of this research revealed that the formation of covalent bonds between the rubber matrix and the nano-particles by the introduction of sulfur at the CNT surface has positive effects on the viscoelastic behavior and the network structure of the rubber compounds, by a decrease of both the loss factor at 60 °C (rolling resistance) and the non-elastic defects, while increasing the crosslink density of the new compounds.