A new method for the tuning and enhancing photoluminescence (PL) characteristics of light emitting poly (3-methylthiopnehe) (P3MT) nanotubes through E-beam irradiation under atmospheric environments is reported. An E-beam generated from a linear electron accelerator (1 MeV, 1.6 × 1013–8.0 × 1016 electrons cm–2) is irradiated onto P3MT nanotubes including an Al2O3 template. From laser confocal microscope (LCM) PL experiments, significant enhancements in the PL intensity—up to about 90 times of an isolated single strand of the E-beam irradiated P3MT nanotubes—are observed. The luminescent color of the P3MT nanotubes changes from green to red color depending on the variation of E-beam dosage. These results might originate from the de-doping effect and the conformational modification through E-beam irradiations. Conformational changes of the E-beam irradiated P3MT nanotubes are confirmed by LCM single Raman and ultraviolet-visible (UV/Vis) absorption spectra. From UV/Vis absorption spectra, it is observed that the π–π* transition peak and the doping induced bipolaron peaks of the P3MT nanotubes dramatically vary with E-beam irradiating conditions.