Two sulfonated polyimide (SPI) thin films were prepared with water and THF/water mixed solvents, respectively. The SPI thin film prepared with THF/water showed more than 5 times higher proton conductivity than that prepared with water mixed solvent at low relative humidity (RH) and 298 K. In this study, polarized optical microscopy (POM), grazing incidence small angle X-ray scattering (GISAXS), and p-polarized multiple angle incidence resolution spectrometry (pMAIRS) were carried out to investigate liquid crystalline (LC) optical ordered structure, organized structure, and molecular orientation. The molecular ordered parts using LC properties in the SPI thin films exhibited an almost identical structure under the low RH condition. On the other hand, the molecular orientation of the imide C=O groups in the non-ordered parts, which could not be detected by POM and GISAXS, showed different angles. The proton conductivity under low RH conditions is affected by the degree of the molecular orientation in the non-ordered parts of the SPI thin films.