Biodegradable polymers are a green alternative to apply as the base membrane materials in versatile processes. In this study, two dense membranes were made from biodegradable PGS (poly(glycerol sebacate)) and APS (poly(1,3-diamino-2-hydroxypropane-co-polyol sebacate)), respectively. The prepared membranes were characterized by FE-SEM, AFM, ATR-FTIR, TGA, DSC, water contact angle, and degree of swelling, in comparison with the PDMS (polydimethylpolysiloxane) membrane. In the pervaporation process for five organic solvent/water systems at 37 °C, both biodegradable membranes exhibited higher separation factors for ethanol/water and acetic acid/water separations, while the PDMS membrane attained better effectiveness in the other three systems. In particular, a positive relationship between the separation factor and the swelling ratio of organic solvent to water (DSo/DSw) was noticed. In spite of their biodegradability, the stability of both PGS and APS membranes was not deteriorated on ethanol/water pervaporation for one month. Furthermore, these two biodegradable membranes were applied in the pervaporation of simulated ABE (acetone-butanol-ethanol) fermentation solution, and the results were comparable with those reported in the literature.