Lignin derived from lignocellulosic biomass is the largest source of renewable bioaromatics present on earth and requires environmentally sustainable separation strategies to selectively obtain high-value degradation products. Applications of supramolecular interactions have the potential to isolate lignin compounds from biomass degradation fractions by the formation of variable inclusion complexes with cyclodextrins (CDs). CDs are commonly used as selective adsorbents for many applications and can capture guest molecules in their internal hydrophobic cavity. The strength of supramolecular interactions between CDs and lignin model compounds that represent potential lignocellulosic biomass degradation products can be characterized by assessing the thermodynamics of binding stability. Consequently, the inclusion interactions of β-CD and lignin model compounds G-(β-O-4')-G, G-(β-O-4')-G (guaiacylglycerol-β-guaiacyl ether), and G-(β-β')-G (pinoresinol) were investigated empirically by electrospray ionization mass spectrometry and isothermal titration calorimetry, complemented by molecular dynamics (MD) simulations. Empirical results indicate that there are substantial differences in binding stability dependent on the linkage type. The lignin model β-β' dimer showed more potential bound states including 1:1, 2:1, and 1:2 (guest:host) complexation and, based on binding stability determinations, was consistently the most energetically favorable guest. Empirical results are supported by MD simulations that reveal that the capture of G-(β-β')-G by β-CD is promising with a 66% probability of being bound for G-(β-O-4')-G compared to 88% for G-(β-β')-G (unbiased distance trajectory and explicit counting of bound states). These outcomes indicate CDs as a promising material to assist in separations of lignin oligomers from heterogeneous mixtures for the development of environmentally sustainable isolations of lignin compounds from biomass fractions.