The addition of dimethylsulfoxide and Zonyl into poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS) can be combined to achieve excellent electrical, optical, and mechanical properties. We demonstrate that it is possible to produce highly transparent conducting electrodes (FoM > 35) with low Young's modulus and high carrier density. We investigated the relationship between the transport properties of PEDOT:PSS and the morphology and microstructure of these films by performing Hall effect measurement, atomic force microscopy, and grazing incidence wide-angle X-ray scattering (GIWAXS). Our analysis reveals the distinctive impact of the two additives on the PEDOT and PSS components in the solid-state PEDOT:PSS films. Both additives induce fibrillar formation in the film, and the combination of the two additives only enhances the fibrillary nature and the aggregations of both PEDOT and PSS components of the film. In situ GIWAXS allows to time-resolve the morphology evolution. Our analysis reveals the influence of additives on the aggregation and self-assembly behaviors of the PEDOT and PSS components. Aggregation occurs during the transition from wet to dry film, which is observed exclusively during the thermal annealing step of the as-cast hydrated film. These results indicate that the additives directly influence the self-assembly behaviors of PEDOT and PSS during the ink-to-solid phase transformation of the hydrated film, which occurs primarily during the initial seconds of post-deposition thermal annealing.