Microporous covalent organic frameworks (COFs) hold great potential for small molecule separation but are yet challenging to design and synthesize. Here we report a framework interpenetration strategy to make microporous COFs for efficient separations of C8 alkyl-aromatic isomers. Two pairs of microporous three-dimensional (3D) salen- and Zn(salen)-based COFs are prepared by Schiff-base condensation of ethanediamine with tetrahedral tetra(salicylaldehyde)-silane or -methane derivatives in the presence or absence of metal ions. The four 3D COFs are isostructural and have a 7-fold interpenetrated diamondoid open framework with less than 8.0 Å wide tubular channels. They exhibit permanent porosity, high thermal stability, and good chemical resistance. The two COFs functionalized with uncoordinated salen groups can serve as stationary phases for high-performance liquid chromatography to provide baseline separation of xylene isomers and ethylbenzene with excellent column efficiency and precision, whereas the COFs with Zn(salen) motifs cannot achieve high-resolution separation. The salen-COFs showed high affinity to the o-xylene, allowing fast and selective separation of the o-isomer from the other isomers within 7 min. This is the first report utilizing COFs to separate the practically important aromatic isomers. This work highlights new opportunities in designing microporous COFs and paves the way to expand the potential applications of COF materials.