The invention relates to a composition for curing gastrointestinal functional disorders, a preparation method thereof and an application thereof in preparing drugs for curing the gastrointestinal functional disorders. The bulk drugs of the composition comprise radix bupleuri, radix glycyrrhizae preparata, fruit of immature citron and white paeony root, which follow a weight proportion of 6:6:6:6-9. The composition comprises the following components by weight percent: 24.5-46.5% of total flavonoids, 10.5-31.6% of total saporins, 17.0-35.4% of naringin, 1.1-8.5% of glycyrrhizic acid and 3.2-13.7% of paeoniflorin. The preparation method is as follows: condensing water solution of the bulk drugs; using macroporous absorption resin for absorption, continuing to wash till the state of colorlessness after the water solution completely passes through a resin column; using 50-85% by weight of ethanol for elution, and collecting eluent; reducing the pressure of solvent, recovering the solvent, drying the solvent, and finally obtaining the composition. Compared with decoction and western medicines, the extract of the composition achieves better and more obvious effect in curing the gastrointestinal functional disorders.