Polyelectrolyte multilayer thin films, assembled by sequentially depositing bilayer (BL) of poly(allyamine hydrochloride) (PAH) and double-walled carbon nanotubes (DWNT) stabilized in polyacrylic acid (PAA) using the layer-by-layer assembly technique, are studied in an effort to establish the relationships between the conformational changes and thermoelectric performances. Controlling the charge density of weak polyelectrolytes with assembly pH conditions gives rise to a different physical, structural, and mechanical properties. The 7.5PAH/3.5 (DWNT-PAA) films exhibit an exponentially-grown thickness behavior due to in-and-out diffusion of the partially charged polyelectrolytes with coiled polymeric conformation, which results in randomly distributed nanotubes within the multilayers. Films made with the same sequences, but with extended polymeric conformation due to high charge density along the polymer chain (PAH at pH 6 and PAA at pH 6.5), show the linear growth behavior with a uniformly oriented nanotube structure and relatively higher elastic modulus. The precise control of the polymeric conformation upon charge density at the nanoscale level significantly affects the thermoelectric performances. A 14 BL 6PAH/6.5(DWNT-PAA) film exhibits an electrical conductivity of 417 S cm-1 and Seebeck coefficient of 85 mu V K-1. This translates to a power factor of 301 mu W m-1 K-2, which is 75 times higher than the same films made at pH 7.5/3.5.