In this work, polyhedral oligomeric silsesquioxane (POSS) with two different functional groups, octa(nitrophenyl)silsesquioxane (ONPS) and octa(aminophenyl)silsesquioxane (OAPS), was incorporated with polydimethylsiloxane (PDMS), forming composite membranes for furfural recovery via pervaporation process. The addition of POSS had enhanced the hydrophobicity of the PDMS and improved the affinity of furfural with membranes. At the same filler loading, OAPS/PDMS membrane showed a superior separation factor to the bare PDMS and the ONPS/PDMS composite. The effects of OAPS loading on property and pervaporation performance of the membrane were also investigated. The loading at 15 wt% was found to be the optimum value that could improve water contact angle to 116° and furfural affinity to achieve over 20% improvement in both furfural flux and separation factor. The PDMS membrane with 15 wt% of OAPS could provide 7-fold concentrated furfural solution compared to the feed. The newly developed OAPS/PDMS membrane showed great potential for furfural recovery as the alternative separation method with improved energy-effectiveness and low chemical footprint.