The separation of BTEX [benzene, toluene, ethylbenzene (EB), and xylene isomers] poses a huge challenge in the industry, attributed to their similar structures and physical properties. Supramolecular compounds show great promise for hydrocarbon separation. Herein, we designed two pairs of endofunctionalized amide naphthotubes with methyl and benzyl side chains, which were first employed as chromatographic separation materials and exhibited high shape-selectivity for BTEX. In particular, the amide naphthotubes with methyl side chains provided complete separation toward BTEX and anti-3a showed high selectivity for the p-xylene over other isomers with α PX/OX = 9.34, α PX/MX = 5.50, and α PX/EB = 4.30. The mechanism of BTEX separation originates from the synergistic effect of specially confined tandem N−H•••π and C−H•••π interactions toward aromatic compounds. The findings of this research show promise for practical applications in efficiently separating crucial aromatic isomers.