To isolate and identify the prototype constituents absorbed in rat serum of citrus aurantium L. after oral administration of Dachengqi Decoction (DT) based on the preliminary research of Serum Pharmacochemistry of DT. Extracts of citrus aurantium L. were isolated and purified targeted by silica gel chromatography based on serum fingerprints. The prototype constituents absorbed in rat serum of citrus aurantium L. were screening and determined according to their retention time and UV absorption spectra and their structures were identified according to relevant spectra data. Two original ingredients absorbed in blood of citrus aurantium L. from Dachengqi Decoction were isolated and identified as Naringenin and 1H-Pyrrole-2-carboxylic acid (Minaline). The original ingredients absorbed in rat serum of citrus aurantium L. after oral administration of Dachengqi Decoction were isolated and identified successfully by introducing Serum Pharmacochemistry into the field of compound separation and preparation.