Electron beam (EB) irradiation is a powerful technology for molecular regulation and electronic structure m o d i fi c a t i o n o f p o l y m e r m a t e r i a l s . P o l y ( 3 , 4ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) films were irradiated under 10 MeV EB by tailoring the dosage from 2.5 to 160 kGy. An intriguing phenomenon occurs in the electrical conductivity (σ) of PEDOT:PSS, where it increases first and then reduces in all the low (2.5−30 kGy), medium (30−100 kGy), and high (100−160 kGy) dosage regimes, while the Seebeck coefficient nearly remains constant. The maximum σ and power factor (PF) values of irradiated PEDOT:PSS are both about 2.5 times of those of pristine PEDOT:PSS. Dominant cross-linking promotes thermal conductivity and mechanical stability, while chain scission leads to their reduction. Structural analysis and DFT computational results have revealed that oxygen containing functional groups can be easily introduced into insulating PSS chains during irradiation, which lowers band gap energy and contributes to the enhancement of the thermoelectric performance of PEDOT:PSS. Besides, the conformation changes of PEDOT from neutral (benzoid) to oxidized (quinoid) form also benefit the carrier transport of PEDOT:PSS. The findings shed light on the modification effect of EB on conducting polymers and provide an innovative treatment and considerable reference for the universal construction of conducting polymer systems with high thermoelectric performance.