The advantages of designability, functionalizability, and tailorability makes covalent organic frameworks (COFs) promising for separation application. Here, we propose a strategy to improve the performance of gas chromatography for the separation of isomers by tuning the topology of two-dimensional (2D) COFs. 2,5-Diaminobenzotrifluoride (Pa-CF 3 ) with trifluoromethyl functional group was selected to condense with biphenyl-3,3′,5,5′-tetracarbaldehyde (BTA) possessing D 2h symmetry, and 1,3,5-benzenetricarboxaldehyde (Tb) possessing C 3 symmetry, respectively, to prepare heteropore BTAPa-CF 3 and homopore TbPa-CF 3 . The prepared BTAPa-CF 3 has a richer pore structure and higher density of the trifluoromethyl functional group than TbPa-CF 3 . The abundant pore sizes of the heteropore structure and dipole forces of the trifluoromethyl functional group gave the BTAPa-CF 3 bonded capillary column better performance than the TbPa-CF 3 bonded capillary column for the separation of hexane, heptane, xylene, chlorotoluene, butylbenzene, and isoamyl acetate isomers with good repeatability. This work provides new idea for designing stationary phases for the separation of isomers from a topological view.