CD-MONs (β-cyclodextrin-based microporous organic networks), derived from β-cyclodextrin, possess notable hydrophobic characteristics, a considerable specific surface area, and remarkable stability, rendering them highly advantageous in separation science. This research aimed to investigate the utility of CD-MONs in chromatography separation. Through a monomer-mediated technique, we fabricated an innovative CD-MON modified capillary column for application in open-tubular capillary electrochromatography (OT-CEC). The CD-MON-based stationary phase on the capillary's inner surface was analyzed using Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM). We assessed the performance of the CD-MON modified capillary column for separation purposes. The microstructure and pronounced hydrophobicity of CD-MON contributed to enhanced selectivity and resolution in separating diverse hydrophobic analytes, such as alkylbenzenes, halogenated benzenes, parabens, and polycyclic aromatic hydrocarbons (PAHs). The maximum column efficiency achieved was 1.5 × 105 N/m. Additionally, the CD-MON modified capillary column demonstrated notably high column capacity, with a methylbenzene mass loading capacity of up to 197.9pmol, surpassing that of previously reported porous-material-based capillaries. Furthermore, this self-constructed column was effectively utilized for PAHs determination in actual environmental water samples, exhibiting spiked recoveries ranging from 93.2 to 107.9% in lake water samples. These findings underscore the potential of CD-MON as an effective stationary phase in separation science.