Single-crystal　covalent　organic　frameworks　(SCOFs)　with　long-range　ordered　crystal　structures　have　emerged　as　potential　separation　media　for　high-performance　liquid　chromatography　(HPLC).　Herein,　capsule-type　SCOFs　(C-SCOFs)　were　synthesized　at　room　temperature　and　directly　utilized　as　a　stationary　phase　for　HPLC.　Owing　to　its　regular　morphology,　excellent　monodispersity,　outstanding　chemical　stability,　organized　pore　structure,　and　pronounced　hydrophobicity,　C-SCOFs　packed　column　could　not　only　efficiently　separate　hydrophobic　molecules　with　outstanding　column　efficiency　but　also　achieved　baseline　separation　of　15　isomers　with　similar　physicochemical　properties,　including　iodoanisole　isomers,　iodotoluene　isomers,　and　iodobenzotrifluoride　isomers.　Especially,　the　column　efficiencies　of　50700-60600　plates/m　were　achieved　for　xylene　isomers　and　the　resolution　values　for　o-/m-xylene　and　m-/p-xylene　were　1.85　and　3.08,　respectively.　In　comparison　with　the　commercial　C18　column　and　the　polycrystalline　COF　packed　column,　the　separation　performance　of　the　C-SCOFs　packed　column　showed　better　advantages　in　isomer　separation.　Furthermore,　the　C-SCOFs　packed　column　was　applied　to　separate　psoralen　and　isopsoralen　from　psoralea　corylifolia　and　the　phthalate　esters　(PAEs)　in　the　river　water　sample,　demonstrating　the　potential　of　C-SCOFs　packed　column　for　practical　applications.　This　study　not　only　promoted　the　development　of　SCOFs　with　unique　structures　as　potential　stationary　phases　for　chromatographic　analysis　but　also　broadened　the　application　of　SCOFs.