Carbon nanotube-based organic thermoelectric composites have garnered a significant amount of research interest due to their synergistic benefits of the high electrical conductivity of carbon nanotubes and the low thermal conductivity of organic materials. Nevertheless, the correlation between the organic molecular structures and the thermoelectric properties of these composite systems has remained largely unexplored. This study delves into the doping effects of radical-containing naphthalene diimides (NDIs) on single-walled carbon nanotubes (SWCNTs) through molecular engineering. It finds that the structures of radical groups crucially impact the frontier energy levels of NDI molecules, thus influencing doping effects on SWCNTs. Conjugated phenoxy radicals enhance p doping, yielding superior n-type thermoelectric properties, while nonconjugated radicals promote n doping, enhancing p-type characteristics. This work highlights the enormous potential of molecular engineering through modulating doping effects for novel TE materials in energy conversion and utilization applications.