Transient isotachophoresis (tITP) is a universal online sample preconcentration technology. It uses ITP to focus electrically charged analytes during the initial stage of capillary electrophoresis (CE) analysis, which can effectively improve the sensitivity of CE. In this work, an approach of tITP under counter-electroosmotic flow was developed for capillary zone electrophoresis (CZE) determination of five trace food additives which include benzoic acid, sorbic acid, sunset yellow, allura red, and amaranth in beverage samples. The parameters that affect the preconcentration effect of the system, such as the type of terminating electrolyte and its injection time, the preconcentration time of ITP, and the sample injection time, have been investigated in detail. The mechanism of counterflow-tITP was explored preliminarily. Under optimal conditions, the sensitivity of five food additives was improved 11.9, 11.5, 13.04, 10.05, and 15.3 times. Their limits of detection (LODs, S/N = 3) reached 0.15, 0.10, 0.38, 0.33, and 0.11 μg/ml, with good repeatability (peak area RSDs ≤ 6.9%) and calibration graph linearity (r ≥ 0.9992). Recoveries of five food additives in spiked beverage samples ranged from 92.0 to 100.8% with RSDs between 1.38 and 2.95%. This method is simple, rapid, and sensitive. It has been successfully applied to the separation and detection of trace food additives in cocktails, orange juice, and carbonated beverages. The feasibility of determination of trace additives in beverages by tITP-CZE under the condition of counterflow has been confirmed.