In recent years, covalent organic frameworks (COFs) play an important role in the field of chromatographic separation. However, COFs are used rarely in open-tubular capillary electrochromatography (OT-CEC) so far, and the reported methods have not been applied to actual sample analysis. Herein, a novel azine-linked COF (N0-COF) coated capillary was prepared as OT-CEC separation channel and a new method for separation and detection of environmental endocrine disruptors, i.e., bisphenol A (BPA) and its analogues was established. Under optimal separation conditions, the analytes were baseline separated by the N0-COF coated capillary with 20 min. The intra-day, inter-day and column-to-column relative standard deviations were 0.07–2.99%, 1.05–3.20% and 1.31–5.83% for the migration time; 1.68–5.50%, 1.52–9.24% and 4.04–9.14% for the peak area. The method was further applied to separate and determine BPA and its analogues in beverage samples, and the recovery ranged from 91.0–112.0%.