Six previously undescribed 2, 9-deoxyflavonoids (1/2a, 1/2b, 6, and 7), along with six known compounds (3-5, and 8-10), were isolated from the twigs and leaves of Aglaia odorata. Their structures were determined by a combination of spectral analysis, ECD calculation and enzymatic hydrolysis assay. Surprisingly, (±) aglaindanone E (11a, 11b) were unexpectedly formed as the derivatives of compounds 3-6 when exposed to ambient natural light. Furthermore, the plausible biosynthetic pathway of 2, 9-deoxyflavonoids was proposed and chemically mimicked. In biological activity assay, compounds 1/2a, 1/2b, 4, and 6 showed potential protective effects in the 0.75%CSE-induced BEAS-2B cells injury model.