A series of alcohols (methanol, ethanol and isopropyl alcohol) were added to poly(3,4-ethylenedioxythiophene): (polystyrene sulfonate) (PEDOT: PSS) aqueous solutions in order to manipulate the molecular structure of the PEDOT chains in PEDOT: PSS hole transporting materials (HTMs) and thus to improve the power conversion efficiency of CH3NH3PbI3 based solar cells. The structural and electronic characteristics of the resultant PEDOT: PSS HTMs were analyzed using atomic-force microscopy, contact angle measurement, Raman scattering spectrometry and photoelectron spectrometry. The properties of the PEDOT: PSS thin films could be controlled by tuning the viscosity of the PEDOT: PSS solutions. High viscosity PEDOT: PSS solutions resulted in linear structured PEDOT chains, which increased the work function of the PEDOT: PSS HTMs thereby improving the open-circuit voltage of the CH3NH3PbI3 solar cells. The surface roughness and surface free energy of the PEDOT: PSS HTMs influence the structural properties of CH3NH3PbI3 thin films, which determines the exciton dissociation at the CH3NH3PbI3/PEDOT: PSS interface (short-circuit current density) and the carrier recombination at the CH3NH3PbI3/[6,6]-phenyl-C61-butyric acid methyl ester (PC61BM) interface (fill factor). In addition, it is predicted that the power conversion efficiency can be further improved by increasing the crystallinity of the CH3NH3PbI3 thin film.