Roots of Ophiopogon japonicus have been used as a functional food ingredient and traditional Chinese medicine for a long time in China. Homoisoflavonoids are one of the major kinds of bioactive compounds in O. japonicus; however, literature data about its homoisoflavonoids profile are scarce because of the complex ingredients with low abundance. Here, homoisoflavonoid fraction was prepared by petroleum ether extraction. Then, a high-speed countercurrent chromatography offline coupling with high-performance liquid chromatography-diode array detectorquadrupole time-of-flight tandem mass spectrometry was developed for systematic identification of homoisoflavonoids. After that, 39 homoisoflavonoids, including 29 homoisoflavanone and 10 homoisoflavone, were unambiguously or tentatively identified, while 12 of them were reported in O. japonicus for the first time. Finally, eight available homoisoflavonoids were sensitively, precisely, and accurately determined by standard calibration curves, with limit of detection and limit of quantification in the range of 0.05-0.30 μg/mL and 0.12-0.66 μg/mL, relative standard deviation less than 7.3% for intra-and interday variations, and recovery at 94.5-105.2%. Collectively, our developed method is efficient, reliable, and valuable to profile chemical components of complex natural products.