In this study, ionic liquid based microwave-assisted extraction (IL-MAE) followed by high-performance liquid chromatography (HPLC) was developed for determination of major organic acids in honeysuckle tea. The results suggest that varying the anion and cation had significant effects on the preparative extraction efficiency; aqueous solution of [C6mim]Br was selected as solvent. The optimized extraction parameters were obtained as follows: IL concentration 0.5 M, temperature 50 °C, solvent to material ratio 20:1 mL/g and duration 9 min. Moreover, principal component analysis (PCA) was used to analyze the significances of these factors for IL-MAE and their interactions, and IL concentration was proved to be the most significant parameter. Compared with conventional sample preparation method, the content of organic acids in analytical sample was enhanced about 1.5-fold using IL-MAE in a shorter duration. In addition, a kinetic model of the preparative extraction process was established to fit the experimental data (R2 > 0.99). The proposed HPLC method was successfully applied for determination of 5 organic acids in honeysuckle tea. The present research supported necessary data for sample preparation and quality analysis of honeysuckle tea.