The objective of this work is to study the adsorptive separation of the biomass-derived furfural (Fur) and 5-hydroxymethylfurfural (5-HMF). Because Fur and 5-HMF have similar ellipsoidal shapes, the diffusion of the larger 5-HMF may be blocked by the elliptical window of adsorbents. Thus, two zeolitic imidazolate framework (ZIF) materials with the identical chemical composition, MAF-6 and MAF-5, were used as spherical and ellipsoidal pore adsorbents, respectively. In the dynamic column adsorption of a binary-component system (Fur/5-HMF, 5/5 wt %) in an aqueous solution, the adsorption amounts of Fur on MAF-6 display a 13% decrease compared with the single-component system, whereas the adsorption amounts of Fur on MAF-5 are identical to those obtained in the single-component system and the amounts of adsorbed 5-HMF are almost negligible. Thus, the Fur/5-HMF selectivity is only 6.4 for MAF-6, whereas the selectivity reached 115.8 for MAF-5. The results show that the narrow elliptical window/ellipsoidal tile of MAF-5 enhanced separation selectivity compared with the larger circular window/spherical cage of MAF-6. In addition, the general rate model and density functional theory calculations further verify that the elliptical window of MAF-5 exhibits a strong mass-transfer barrier that must be overcome for the diffusion of the larger 5-HMF molecules.