The invention relates to an ion-pair compound of chelerythrine from Chinese medicine extracts, a preparation method and application thereof. Organic acids of the invention mainly comprise chlorogenic acid, gallic acid, shikimic acid, oleanolic acid, ursolic acid, benzoic acid, salicylic acid, tartaric acid, lactic acid, sorbic acid, fumaric acid, malic acid, citric acid, maleic acid, glycyrrhizic acid, glycyrrhetinic acid, carnosic acid, P-hydroxycinnamic acid, rosmarinic acid, succinic acid, ferulic acid, protocatechuic acid, cinnamic acid, caffeic acid, chicoric acid or cortex pseudolaricis acetic acid. The ion-pair compound prepared from the chelerythrine and the organic acids has the antibacterial biological activity. The invention relates to the application of the ion-pair compound of the chelerythrine to medicine, animal remedy or daily use cosmetics.