To extend the application of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) in liquid food, and to improve the physicochemical stability, we prepared stable DHA and EPA nanoemulsions, which can be used for large scale production. The Emulsion Phase Inversion (EPI) method was used to prepare nanoemulsions as safe and convenient with low-energy emulsification method. The type of oil, the type of surfactant and the concentration of surfactant have the most significant effect on particle size. Within 20 days, the nanoemulsions have good physical stability under different storage conditions, and the retention rate of DHA/EPA can be stabilized at >60%. Furthermore, different types of natural antioxidants were added and the effect was detected by analyzing the peroxide value. Among them, tea polyphenols showed the most significant effect. The data obtained showed enhanced nanoemulsions stability, increased application in food and actual large-scale production.