The growing demand for flexible, lightweight, and highly processable electronic devices makes high-functional conducting polymers such as poly (3,4-ethylene dioxythiophene): polystyrene sulfonate (PEDOT:PSS) an attractive alternative to conventional inorganic materials. However, considerable improvements are necessary to make conducting polymers a commercially viable choice. This study explores nanopatterning, as an effective strategy for enhancing polymer functionality, which results in substantial improvements in mechanical, thermal, optical, and electrical properties. Nanopatterned conducting polymers with manipulated electrical properties can be utilized in various fields, including thermoelectrics (TE). Introducing nanopatterning into thermoelectric polymers is challenging due to intricate technical hurdles and the necessity for individually manipulating the TE parameters such as electrical conductivity, Seebeck coefficient, and thermal conductivity. Here, enhanced TE performance is achieved by imposing array nanopatterns on PEDOT:PSS free-standing films using direct electron beam irradiation. Through nanopatterning, selective and independent control of electric and thermal transport in PEDOT:PSS was achieved. The e-beam irradiation transformed PEDOT:PSS from a highly-ordered quinoid to an amorphous benzoid structure, leading to a remarkable reduction in the thermal conductivity by 70% of that of the non-patterned PEDOT:PSS, without a significant reduction in electrical conductivity. Consequently, the thermoelectric figure of merit was enhanced by 60% compared to non-patterned PEDOT:PSS. The proposed nanopatterning methodology demonstrates a skillful approach to precisely manipulate the thermoelectric parameters, thereby improving the thermoelectric performance of conducting polymers, and promising utilization in cutting-edge electronic applications.