Paeonia ostii seed oil, rich in polyunsaturated fatty acids (PUFAs), offers a valuable source of health-promoting vegetable oils. However, the metabolic mechanisms underlying PUFA content variation and biosynthesis regulation remain poorly understood. This study analyzed PUFA variation patterns in seeds from 131 P. ostii plants using gas chromatography-mass spectrometry (GC-MS). To investigate primary metabolite dynamics, ultra-high-performance liquid chromatography (UPLC)-MS was conducted on seeds at key developmental stages 2 and 4, identifying 422 primary metabolites, including 165 differential ones. Pearson correlation analysis revealed that abscisic acid (ABA) was highly associated with fatty acids and their derivatives. Exogenous ABA treatment significantly increased PUFA content in P. ostii seeds. Furthermore, overexpression of ABSCISIC ACID-INSENSITIVE 5 (PoABI5) in Arabidopsis thaliana upregulated key genes, including AtFAD2/3 and AtWRI1, enhancing PUFA accumulation. This research elucidates key metabolites, particularly PUFAs, in mature seeds of various cultivated plants and developing seeds of P. ostii. Moreover, this study reveals the role of ABA and ABI5 in PUFA biosynthesis and provides a foundation for metabolic engineering to improve oil crop quality, addressing nutritional demands, particularly for populations with metabolic syndromes.