This study explores the enhancement of thermoelectric performance in carbon nanotubes (CNTs) via targeted sulfur doping at the central region of the nanotube structure. Carbon nanotubes exhibit very good electrical conductivity, providing unique advantages at the nanoscale. However, CNTs have very high thermal conductivity which limits the thermoelectric efficiency, measured by the value of merit (ZT). To explore this mechanism of CNT doping, a multi-scale computational study has been developed using the density functional tight binding (DFTB) and non-equilibrium Green’s function (NEGF) formalism to study the effect of sulfur addition on the electronic structure of each single-walled CNT and the phonon transport properties of the CNT. Computational studies show that sulfur dopants introduce localized electronic states near the Fermi level that significantly increase the Seebeck coefficient while preserving the high electrical conductivity of CNTs. The sulfur atoms also act as phonon scatterers, thereby spreading the heat flux and reducing the thermal conductivity of the lattice while scattering phonons. The combination of these electronic and phononic improvements results in significant improvements in the ZT values of typical thermoelectric-based cycles. These results provide a practical route to effectively reduce interdependent thermoelectric parameters, and inform the future development of CNT-based materials for new energy conversion applications.