The objective of present study was to simultaneously isolate of isoflavone and soyasaponin compounds from the germ of soybean seeds. Soy germ flours were defatted with hexane for 48h at room temperature, and methanolic extracts were prepared using reflux apparatus at $90^{\circ}C$ for 6h, two times. After extraction, extracts were separated with preparative RP-$C_{18}$ packing column ($125{\AA}$, $55-105{\mu}m$, $40{\times}150mm$), and collected 52 fractions were identified with TLC plate (Kieselgel 60 F-254) and HPLC, respectively. Among the identified isoflavone and soyasaponin fractions, isoflavone fractions were re-separated using a recycling HPLC with gel permeation column (Jaigel-W252, $20{\times}500mm$). Final fractions were air-dried, and the purified compounds of two isoflavones (ISF-1-1, ISF-1-2) and four soyasaponins (SAP-1, SAP-2, SAP-3, SAP-4) were obtained. Two isoflavone compounds (ISF-1-1, ISF-1-2) were acid-hydrolyzed for the identification of their aglycones, and confirmed by comparing with 12 types of isoflavone isomers. While the four kinds of soyasaponins were identified by using a micro Q-TOF mass spectrometer in the ESI positive mode with capillary voltage of 4.5kV, and dry temperature of $200^{\circ}C$. Base on the obtained results, it was conclude that ISF-1-1 is the mixture isomers of daidzin (43.4%), glycitin (47.0%), and genistin (9.6%), but ISF-1-2 is the single compound of genistin (99.8% <). On the other hand, soyasaponin SAP-1 is the mixture compounds of soyasaponin A-group (Aa, Ab, Ac, Ae, Af); SAP-2 is soyasaponin B-group (Ba, Bb, Bc) and E-group (Bd, Be); SAP-3 is soyasaponin B-group (Ba, Bb, Bc), E-group (Bd, Be), and DDMP-group (${\beta}g$); SAP-4 is soyasaponin B-group (Ba, Bb, Bc), E-group (Bd, Be), and DDMP-group (${\beta}g$, ${\beta}a$), respectively.