Objective A targeted metabolomics based on gas chromatography-mass spectrometry (GC-MS) was established for the authentication of sea duck eggs. Methods In this study, gas chromatography-mass spectrometry was used to characterize the fat acid profiles of sea duck eggs and cage duck egg s. Chemometrics was used to analyze the difference between sea duck eggs and cage duck eggs to screen the markers that could be used to identify the authenticity of sea duck eggs. Results Omega-3 fatty acids (Ω-3) in sea duck eggs account for a higher proportion of total fatty acids than cage duck eggs, and there were significant differences (t=23.58,P<0.05). Sea duck eggs and cage duck eggs were distinguished by principal component analysis. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were screened by orthogonal partial least squares discriminant analysis that contributed the most to the difference of sea duck eggs and cage duck eggs. EPA was detected only in sea duck eggs, and the content of DHA in sea duck eggs was higher than that of cage duck eggs. Conclusion This study showed that EPA and DHA can be used as a reliable marker to authenticate sea duck eggs.