Polypyrrole (PPy) nanotubes with different diameters have been successfully prepared by different concentrations of oxidant with methyl orange (MO) as template. When the molar ratio of oxidant to pyrrole monomer was 1.5:1, PPy-1.5:1 nanotubes with smooth surface and diameter of 40?60 nm were obtained. The large crystallization orientations of molecular chains in PPy nanotubes due to the template effect of MO significantly enhance π-π interactions, which improves electrical conductivity of PPy-1.5:1 nanotubes. The great degree of conjugation and the small conjugate defect of the molecular chains in PPy-1.5:1 also contribute to high mobility of carriers and high electrical conductivity. The hollow structures introduced to PPy bring about appropriate grain boundary defects and benefit seebeck coefficient of PPy nanotubes. Enhancement of electrical conductivity and seebeck coefficient of the PPy-1.5:1 nanotubes result in the maximization of power factor of 0.55 μWm-1K-2, about 22 orders of magnitude higher than PPy particles prepared under the same condition. By designing and tailoring the polymer structure, nano-structured PPy with high thermoelectric properties are highly expected.