This research explores the influence of crystallinity on gas chromatographic (GC) separation using covalent organic frameworks (COFs) as stationary phases. Three COF materials (CTF-DCBs) with varying crystallinity were synthesized and characterized. CTF-DCB-1, with superior crystallinity, demonstrated high-selectivity GC separation of benzene isomers as well as styrene/phenylacetylene mixtures, while CTF-DCB-2 and CTF-DCB-3 exhibited lower crystallinity and worse separation performance. Thermodynamic and kinetic tests showed that CTF-DCB-1 had the worst thermodynamic adsorption but low diffusion mass transfer resistance, which resulted in the best separation. Therefore, optimizing the crystallinity of COFs is necessary for balancing the kinetic diffusion and thermodynamic interactions towards the analytes, achieving high-performance GC stationary phases.