Two new neolignans, myrifralignans F–G (
14
and
18
), four new diarylnonanoid derivatives, myrifragranones A–D (
21
–
24
), and 18 known compounds were isolated and structurally elucidated from nutmeg (
Myristica fragrans
Houtt.) seeds. The absolute configurations of these secondary metabolites were determined using the electronic circular dichroism technique. The inhibitory potential of these isolated compounds on soluble epoxide hydrolase (sEH) was investigated for the first time. Among them, malabaricones B and C (
19
and
20
) and four new compounds
21
–
24
displayed inhibitory activities against sEH, with IC
50
values ranging from 14.24 to 46.35 µM. Additionally, the binding mechanism, key binding interactions, stability, and dynamic behaviour of the active compounds with the sEH enzyme were analysed using
in silico
molecular docking and dynamics simulations. Our findings suggest that nutmeg could become a promising natural source for discovering and developing new sEH inhibitors.