The chromatographic separation of Centaurea aegyptiaca L. methanolic extract successively yielded four main fractions of different polarities. Among the tested fractions, butanol and ethyl acetate fractions were the most toxic against cotton aphid, A. gossypii using spraying method technique under laboratory conditions after 24 and 72 h of treatment. Application of optimal chromatographic separation of C. aegyptiaca butanol and ethyl acetate fractions afforded six secondary metabolites which were isolated and identified belonging to two main classes flavonol glycosides, the new 6-hydroxy-3-methoxykaempferol-8-O-β-D-glucopyranoside (centaegyin) 1 beside the three 6,8-dihydroxykaempferol-3-O-β-D-glucopyranoside 2, astragalin 3 and populnin 4 those reported from the plant for the first time and two elemanolide sesquiterpenes, methyl 8α-(3,4-dihydroxy-2-methylene-butanoyloxy)-6α,15-dihydroxy-elema-1,3,11(13)-trien-12-oate 5 and methyl 8α,6α,15-trihydroxy-elema-1,3,11(13)-trien-12-oate 6. Assessment of the toxic effect of the isolated compounds, from the active fractions, against A. gossypii revealed that flavonoids 1, 2 and 3 were the active principles in the butanol fraction after 24 and 72 h of treatment. The isolated compounds were structurally identified using various spectroscopic analyses (ESI-MS, 1H-NMR, 13C-NMR, H-H COSY, HSQC and HMBC).