Conjugated polymers are desired as organic electrode materials because of their functional properties such as solution process, low cost, and transparency. Poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS), in particular, shows the highest applicability, but its heterogeneous structure presents limitations in terms of electrical conductivity. In this study, a facile method to fabricate multi-layered thin films with higher ordered structures was developed. Through the etching process with H2SO4 and dimethyl sulfoxide(DMSO), the insulated rich-PSS was removed from the upper layer to improve its electrical properties and rearrange the PEDOT molecular structures. The thickness of PEDOT:PSS thin films was experimentally optimized to maximize the enhancement of carrier mobility via a layer-by-layer (LBL) process. The combined method, consisted of etching and the LBL process, showed the improvement of the charge carrier mobility from 0.62 to 2.80 cm2 V−1 s−1. The morphology and crystallinity of the ordered PEDOT:PSS structure were investigated by X-ray photoemission spectroscopy (XPS), Raman, and X-ray diffraction (XRD). As a result, two-dimensional lamellar-stacked PEDOT:PSS thin films were fabricated through the repetitive etching and LBL process. The optimized PEDOT:PSS thin film showed an excellent electrical conductivity of 3026 S cm−1, which is 3.8 times higher than that of the pristine film (801 S cm−1).