In recent decades, pervaporation membrane separation coupled with fermentation is recognized as a promising process in biofuel production. This review presents the latest progress in membrane materials applied for the biobutanol separation from dilute aqueous solution or fermentation broth. It also summarizes various membrane-based separation processes for in situ recovering biobutanol during the fermentation. Opportunities and challenges in future development of pervaporation organophilic membrane materials and fermentation coupled processes for biobutanol production are outlook.