A comprehensive investigation was conducted on the relationships between molecular structure, morphology and thermoelectric properties of HCl-doped polyaniline (PANi) nanorods subjected to 10[Formula: see text]MeV electron beam irradiation. Morphological and structural characterization revealed that the crystallinity of irradiated PANi nanorods remained almost unchanged, and minimal oxygen content was detected. This resulted in minimal alterations to the thermo-stability. In addition, the thermoelectric properties of PANi were enhanced. A maximum conductivity of 22.85[Formula: see text]S/cm was obtained at 50[Formula: see text]kGy, which was 1.46 times that of pristine PANi. Interestingly, the Seebeck coefficient reached a maximum of −3.56[Formula: see text][Formula: see text]V/K at 100[Formula: see text]kGy, indicating [Formula: see text]-type organic semiconductor properties. However, a peak power factor of 0.024[Formula: see text][Formula: see text]W[Formula: see text]m[Formula: see text] K[Formula: see text] was achieved with 60[Formula: see text]kGy irradiation, which was slightly enhanced compared to 0.018[Formula: see text][Formula: see text]W[Formula: see text]m[Formula: see text][Formula: see text]K[Formula: see text] for pristine PANi. These results demonstrate that PANi exhibits good irradiation resistance after irradiated with a dose of 100[Formula: see text]kGy. Thus, PANi could be used in high-[Formula: see text] ray (electron) environments, such as radioisotope thermoelectric generators (RTGs).