Here we investigate the thermal diffusion behavior of the nonionic microemulsion water/n-decane/pentaethylene glycol monododecyl ether (C12E5). We study the dependence of the Soret coefficient on the structure and composition by infrared thermal diffusion Rayleigh scattering. The form and size of the microemulsion structure is characterized by dynamic light scattering and small angle neutron scattering. The system was examined in the one-phase region between the emulsification failure boundary and the near critical boundary, where oil swollen nanostructures stabilized by an amphiphilic surfactant film are dispersed in a continuous water phase. The size and shape of these structures as well as the interfacial properties of microemulsions can be varied by changing temperature and composition, which allows a systematic study of their influence on the thermal diffusion properties. In addition, we analyze the relationship between the Soret coefficient and the temperature dependence of the interfacial tension as proposed by A. Parola and R. Piazza (Eur. Phys. J. E 2004, 15, 255-263) and find reasonable agreement for spherical microemulsion droplets.