Because of unique properties like permanent porosity, low density and large surface area, covalent organic frameworks are attractive microporous materials as stationary phase for CEC. Among them, COF-TpPa-1 possesses extraordinary chemical stability and common features of covalent organic frameworks. So, COF-TpPa-1 could be a promising material as stationary phase to enhance separation selectivity and tolerate the acid or alkaline electrochromatographic separation conditions. Here, we report the preparation of COF-TpPa-1 modified capillary column by in situ growth for electrochromatographic separation. The immobilization of COF-TpPa-1 on the inner wall of capillary column was confirmed by Fourier transform infrared spectroscopy, scanning electron microscopy and X-ray diffraction. The fabricated COF-TpPa-1 modified capillary column indicated good resolution for the separation of neutral analytes, nonsteroidal anti-inflammatory drugs and food additives in open-tubular CEC mode. Compared with bare capillary column, the COF-TpPa-1 modified capillary column improved separation selectivity remarkably for tested analytes, including hydrophobic, pi-pi and hydrogen bond interactions. Besides, the prepared capillary column showed excellent repeatability and stability. The intraday, interday and column-to-column relative standard deviations of migration time for neutral analytes were less than 3.54%. This work shows enamine-linked covalent organic frameworks have great potential as stationary phases in CEC.