To elucidate the characteristics of fatty acid composition in different tissues of Anguilla japonica before and after their seaward spawning migration, this study measured the fatty acid contents in the muscle, liver, and ovary of eels collected from the Yangtze River Estuary and offshore waters, and analyzed the distribution characteristics and transformation patterns of various fatty acids in different tissues. The results showed that the fatty acid composition in different tissues of eels from both the Yangtze River Estuary and offshore waters was essentially similar. Among all fatty acids, C18:1n9c had the highest proportion, accounting for over 31% of the total fatty acids in each tissue. Comparing different tissues, in eels from the Yangtze River Estuary, the muscle had the highest content of EPA, the liver had the highest content of DHA and EPA+DHA, and the ovary had the highest contents of ARA, n6-PUFA and SFA. In offshore eels, the muscle had the highest contents of C16:1, C18:1n9c and MUFA; the liver had the highest content of C16:0; and the ovary had the highest contents of C18:0, DPA, HUFA, n3-PUFA and PUFA. Comparing eels before and after seaward migration, the contents of C16:0, ARA, n6-PUFA, SFA, and the DHA/EPA ratio in the ovary of Yangtze River Estuary eels were higher than those in offshore eels. Conversely, the contents of C18:0, C16:1, C18:1n9c, EPA, DPA, DHA, EPA+DHA, HUFA, n3-PUFA, MUFA, PUFA, as well as the EPA/ARA, n3/n6 PUFA and PUFA/SFA ratios in the ovary of offshore eels were higher than those in Yangtze River Estuary eels. The ovary of Yangtze River Estuary eels mainly contained fatty acids for energy provision and precursors for long-chain fatty acid synthesis, whereas the ovary of offshore eels had preliminarily accumulated PUFA nutrients required for egg and embryonic development. Thus, the distribution patterns of different fatty acids among tissues are closely related to the seaward spawning migration process of A. japonica. Before migration, eels in the Yangtze River Estuary primarily focus on energy accumulation and liver metabolism; after entering the sea, eels gradually accumulate PUFA such as EPA, DPA+DHA and n3-PUFA as gonads develop. The selective reservation of different fatty acids in the ovary represents a physiological regulation in response to the nutritional demands of gonadal development.