The invention relates to a rheinic acid berberine ion pair compound with a formula (I) structure and a preparation method thereof, comprising the following steps of: (1) preparing a berberine hydrochloride solution, (2) adding rheinic acid or an alkali metal salt of rheinic acid into the solution obtained in the step (1), heating, stirring and fully reacting; and (3) filtering, washing, refining and drying the reaction products to obtain the rheinic acid berberine ion pair compound. The invention further relates to pharmaceutical compositions containing the ion pair compound, wherein the weight of the ion pair compound is 0.1-99.9% that of the compositions. The invention also relates to applications of the ion pair compound and the compositions thereof for preparing medicines for treating bacterial infection, peptic ulcer, diabetes, hyperlipemia, obesity, arthritis, heart failure, arrhythmia, platelet aggregation, hypertension, intestinal adhesion, etc. The rheinic acid berberine ion pair compound can increases lipid solubility of rheinic acid and berberine, and substantially raises a biological utilization degree.