Introduction: the health benefits of omega-3 fatty acids, as well as the high sensitivity of unsaturated fatty acids to oxidation of fish oil, caused the use of encapsulation of fish oil for enriching food products and drugs. Materials and Methods: this study aims to evaluate the physicochemical properties of nano-encapsulated fish oil, and their oxidative stability during storage at 0 and 24% relative humidity conditions. Emulsion was prepared after sonication with wall materials of maltodextrin (M), modified starch (Hi-cap) and whey protein concentrate (WPC) at the ratio of 1: 4 (oil: wall). Emulsion and nano-encapsulated powder properties including emulsion stability, apparent viscosity, powder moisture, encapsulated coefficient, particle size and morphology of nano-capsules were determined. Results: The lowest amounts of creaming and viscosity were observed in M+Hi-cap+WPC and M, respectively. Moisture content in M+Hi-cap showed the highest value. The lowest and highest particle sizes were measured in M+Hi-cap+WPC and M, respectively. Also, the best encapsulation efficiency was obtained for M+Hi-cap+WPC. SEM photographs showed glass-like sheets of encapsulated materials with the freeze-dryer. During 21 days storage at 0 and 24% relative humidity, the results showed an increase in peroxide and anisidine values. The values were higher at 24% than the 0% humidity, and the best results of oxidative stability were observed in M+Hi-cap+WPC treatment. Conclusion: Based on the findings, relative humidity is an effective factor in the oxidation of fish oil nano-capsules. The use of nano-encapsulation is a practical and effective method for increasing the stability of fish oil for enriching the food and promoting human health.