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A simple, comprehensive, and efficient capillary electrophoresis method using a self‐synthesized ionic liquid [N‐methylimidazole‐β‐cyclodextrin] [bromide] as a separation selector was developed for the simultaneous separation and determination of five chlorogenic acid isomers (chlorogenic acid, cryptochlorogenic acid, neochlorogenic acid, isochlorogenic acid A, isochlorogenic acid B). After optimization of separation conditions, the electrolyte solution was 50 mM ammonium acetate buffer containing 0.7% (w/w) ionic liquid [N‐methylimidazole‐β‐cyclodextrin] [bromide] (pH 4.8), 15 kV of the electric field was applied at 25°C, and the detection wavelength was at 237 nm. Under the optimal separation conditions, good linearities were obtained with linear correlation coefficients of the five analytes of 0.9994–0.9998, and the limits of detection and the limits of quantification were 0.6–2.8 and 2.2–9.5 μg/ml. Excellent accuracy and precision were obtained for the five analytes. The intraday and interday precision of standards ranged from 0.5 to 1.3% and from 1.2 to 1.9%. The intraday and interday precision of samples ranged from 1.0 to 1.9% and from 1.2 to 2.6%. The sample recovery rates were between 98.0 and 101.8%. This method was successfully applied for the analysis of five components in Honeysuckle Chinese medicinal preparations. The mechanisms involved in the separation of five analytes by [N‐methylimidazole‐β‐cyclodextrin] [bromide] were discussed.

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