From the male flowers of Ginkgo biloba L., 26 compounds were isolated and identified including 7-O-(β-d-glucopyranosyloxy)-5-hydroxy-1(3H)- isobenzofuranone (1), piperoside (2), 3-(4-hydroxy-3-methoxyphenyl)propane-1, 2-diol (3), ginkgolide B (4), ginkgolide C (5), hexyl-β-getiobioside (6), benzyl-β-d-xylopyranosyl-(1 → 6)-β-d-glucopyranoside (7), ginkgolic acid (8), kaempferol-3-O-[6′′′-O-p-coumaroyl-β-d-glucopyranosyl-(1 → 2)-α-l-rhamnopyrano-side] (9), quercetin-3-O-[6′′′-O-p-coumaroyl-β-d-glucopyranosyl-(1 → 2)-α-l-rhamnopyranoside (10), apigenin-7-O-β-d-glucoside (11), kaempferol-3-O-α-l-rhamnoside (12), kaempferol-3-O-rutinoside (13), quercetin-3-O-β-d- glucopyranoside (14), quercetin-3-O-α-l-rhamnoside (15), isorhamnetin-3-O-rutinoside (16), kaempferol-7-O-β-d-glucopyranoside (17), kaempferol-3-O-β-d-galactoside-4′-O-β-d-glucoside (18), isorhamnetin-3-O-β-d-glucopyranoside (19), rutin (20), kaempferol-4′-O-β-d-glucopyranoside (21), argaminolic A (22), 4,4′-dihydroxy-3,3′-imino-di-benzoic acid (23), nicotinamide (24), uracil (25), and capilliplactone (26). Among them, compounds 1, 2, 6, 7, 22, 23, and 26 were found in the class Ginkgopsida for the first time. Compounds 8, 11, and 21 showed better active inhibitory effects on NO production among the tested compounds. Compounds 8 and 11 also showed cytotoxicity on three cancer cells. Our phytochemical study of G. biloba flowers enriched the diversity of Ginkgo chemical compositions and may broaden its application in phytotherapy.