In present study, a method basing on accurate mass and fragmentation pattern was designed to screen the terpene lactones and flavonoids in the methanol extract of Ginkgo biloba capsule powder. An UPLC with a hybrid linear ion trap-orbitrap mass spectrometer (UPLC-LTQ-Orbitrap Elite) was used. The chromatographic analysis of the sample was performed on a C 18 column (100 × 2.1 mm ID, particle size 1.9 μm) with gradient elution using methanol and water with 0.10% formic acid. Mass spectrometry was performed in the negative ESI mode. By comparison the accurate mass, element composition and fragment pattern, twenty-six compounds were identified, including 5 ginkgo terpene lactones (bilobalide, ginkgolide A, B, C and J) and 21 flavonoid glycosides. The major glycosides identified included: kaempferol-3-O-glu-glu-rha, kaempferol-7-O-rutinoside, isorhamnetin-3-Orutinoside, kaempferol-3-O-rha-glu, quercetin-3-O-glucoside, kaempferol-3-O-rha-glu-coumaroyl and 3'methoxymyricetin-3-O-rutinoside. The structural isomers were differentiated through the characteristic ions obtained from their MS/MS spectra. In addition, a compound 3,5,4'-trihydroxyflavone-3-O-glucoside, which was not reported in G. biloba before to our knowledge, was identified in the extract. The fragmentation pathways and characteristic product ions of flavonoid glycosides were shown and summarized for the rapid identification. The developed method was proved to be useful and precise for fast qualitative analysis of flavonoid compounds in mixture.