Objective To compare the chromatographic profiles and contents of three flavonoid aglycone equivalents (quercetin, genistein, and kaempferol) in the fruits of Sophora japonica var. pendula Loud. and the authentic Fructus sophorae, so as to provide a theoretical basis for using the fruit of Sophora japonica var. pendula Loud. as a substitute for Fructus sophorae. Methods The fruits of Sophora japonica var. pendula Loud. were collected from different areas of Shijiazhuang in Winter. The flavonoids in the fruits were extracted by successive extraction with methanol. The acidic-hydrolyzed extracts were separated on a Diamonsil C18 column (150 mm×4.6 mm, 5 μm). 0.4% phosphoric acid-methanol (5050, V/V) was used as mobile phase. The flow rate of mobile phase was 1.0 ml/min and the effluents were monitored at 360 nm. Results The chromatographic profiles of the two fruit extracts were consistent basically. The contents of quercetin, genistein, and kaempferol in the fruits of Sophora japonica var. pendula Loud. were (0.30±0.07)%, (3.04±0.27)%, and (2.74±0.30)%, respectively, which were similar to those in the authentic Fructus sophorae. Conclusion It is found that the contents of major flavonoid aglycones in the fruit of Sophora japonica var. pendula Loud. are similar to those in the authentic Fructus sophorae, making it a potential substitute for the Fructus sophorae.