Eight new khayanolides, named thaixylomolins G-N (1-8), two new phragmalins (9 and 10), and two new mexicanolides (11 and 12) were obtained from the seeds of the Trang mangrove plant Xylocarpus moluccensis. The absolute configurations of these limonoids, except for the stereocenter at C-6 of 11 and 12, were assigned by experimental and TDDFT calculated electronic circular dichroism spectra. The khayanolides may be classified into two subclasses, one of which has a C-2 carbonyl and a 3β-acetoxy group, whereas the other possesses a 2β-acetoxy and a C-3 carbonyl function. Khayanolides, rearranged phragmalin-type limonoids, are reported for the first time from plants of the mangrove genus Xylocarpus. The structure of moluccensin J, a known 30-ketophragmalin containing a Δ(8(14)) double bond, was revised to be a khayanolide, named thaixylomolin K. The antiviral activities of the isolates against pandemic influenza A virus (subtype H1N1) were tested by the assay of cytopathic effect inhibition. Three khayanolides, viz., thaixylomolins I, K, and M, exhibited moderate anti-H1N1 activities. The most potent one, thaixylomolin I (IC50 = 77.1 ± 8.7 μM), showed stronger inhibitory activity than that of the positive control, ribavirin (IC50 = 185.9 ± 16.8 μM).