To develop hybrid materials with strong affinity for 2-phenylethanol (2-PE), β-cyclodextrin-based metal-organic frameworks (β-CD-MOFs) were fluorinated using 1H,1H,2H,2H-perfluorooctyltriethoxysilane (13F) via silanol condensation. Subsequently, rutin (represented as LD) was grafted onto the fluorinated β-CD-MOFs through nucleophilic substitution and silanol condensation reaction to prepare L-13F-βMOFs. L-13F-βMOFs were added to polydimethylsiloxane (PDMS) matrix to prepare mixed matrix membranes for 2-PE pervaporation separation. The chemical structure and morphology of the filler were characterized by FTIR, XPS, and SEM. The chemical composition, cry stalline structure, and hydrophilicity/hydrophobicity of mixed matrix membranes were characterized by ATR-FTIR, solvent uptake measurements and contact angle analysis. Meanwhile, the effects of membrane preparation and separation process conditions on pervaporation performance were optimized, and the effect of maltol in the separation of 2-PE in a ternary system was investigated to explore competitive adsorption and permeation. Furthermore, the 2-PE separation mechanism of mixed matrix membranes was investigated. The as-prepared mixed matrix membranes demonstrated a total flux of 1398 g·m-2·h-1, a separation factor of 32.67, and a pervaporation separation index of 44270 g·m-2·h-1. These values are 1.69, 2.74, and 4.95 times higher than those of the pure PDMS membrane, and 1.47, 1.78, and 2.61 times of the PDMS-based mixed matrix membranes with added β-CD-MOFs, respectively. This performance enhancement is attributed to the hydrophilic/hydrophobic interactions, π-π interactions, and hydrogen bonding between the —Si—O—, phenyl rings, and F atomics in L-13F-βMOFs and 2-PE, which improve the affinity for 2-PE. When the concentration of maltol in the feed solution increased to 1.2×10-3, the 2-PE flux and 2-PE/water separation factor of mixed matrix membranes decreased by only 19% and 21%, respectively, indicating excellent molecular recognition capability for 2-PE. During a 168 h stability test, the separation performance of the mixed matrix membranes showed no significant changes, demonstrating the great potential for 2-PE separation applications.