The effect of droplet size on the oxidative stability of triacylglycerol (TAG)-in water emulsion was examined. Microchannel (MC) emulsification was used to make monodispersed emulsion of soybean oil TAG and fish oil TAG with different droplet size. The main polyunsaturated fatty acids (PUFA) of soybean oil TAG and fish oil TAG were linoleic acid (LA; 53%) and docosahexaenoic acid (DHA; 37.3%), respectively. Oxidation was induced by the addition of 2,2’-azobis(2-amidinopropane)-dihydrochloride (AAPH) or ferrous ion. The oxidative stability was followed by the decrease in the oxygen consumption in the solution, peroxide formation, and decrease in the unoxidized PUFA during oxidation, indicating that the oxidative stability of fish oil TAG increased with decreasing the droplet size, while the reverse effect of the droplet size was observed on the oxidation of soybean oil TAG. The decrease in the droplet size induces the increase in the droplet interface, from which the oxidation proceeds to the oil droplet interior. DHA in fish oil TAG would take highly protective interface against oxidative attack of free radicals and metal ions, whereas LA in soybean oil TAG would be more easily oxidized at the interface because of its less protective conformation. The reverse effect of the droplet size on fish oil TAG and soybean oil TAG could be explained by the different interface conformation of both TAG.