The long-chain omega-3 polyunsaturated fatty acids (ω-3 PUFAs) eicosatetraenoic acid (EPA) and docosahexaenoic acid (DHA) are known to play roles in supporting human health, primarily by reducing inflammation and promoting its resolution. In this study, the impacts of EPA/DHA ratios (5.13/1, 2.45/1,1.34/1) on lipid oxidation and digestion behaviors were explored using an in vitro digestion model. Emulsions were characterzied by droplet size, zeta-potential as well as microstructure. Additionally, the release of free fatty acids (FFAs), lipid hydroperoxides (LPO) and thiobarbituric acid reactive substance (TBARS) were also investigaed throughout simulated digestion phases. Notably, for all EPA/DHA ratios, from saliva fluid to gastric fluid, droplet size was slightly changed, accompanied by a significant decrease in absolute zeta-potential, followed by an increase in both parameters after intestinal digestion. Emulsions with the lowest ratio of EPA/DHA (i.e., 1.34/1) exhibited lower FFA release compared to those with higher ratios (i.e., 5.13/1 and 2.45/1). Conversely, the lowest EPA/DHA ratio increased oxidation during the intestinal phase, as indicated by elevated LPO and TBARS levels. This study clearly suggests that EPA/DHA ratios influence the oxidative stability of fish oil emulisions during digestion and provides useful information to formulate fish oil supplementation that improves in vivo oxidative status.