Inverse gas chromatography is a versatile and effective method for the characterization of the solubility thermodynamics and diffusion kinetic of solvent–polymer system with the advantages of fast, low dosage of samples and large range of temperature. Polydimethylsiloxane (PDMS) is well known as an excellent polymer membrane material for its high permeability to gases and liquids and widely used in the separation and purification of bio-fermentation broth which was mainly consisted by acetone, butanol, ethanol and water. In this paper, the inverse gas chromatography method was applied to measure solubility thermodynamics parameters like the infinite dilution activity coefficient and Flory–Huggins interaction parameter between those small molecules and PDMS. The infinite dilution diffusion coefficients were calculated by Van Deemter model over a temperature range of 373.2–413.2K. The diffusion coefficient was fitted with the temperature according to the Arrhenius correlation. The data could help the selection of membrane material in pervaporation or gas separation and the analysis of mass transfer process.