Flaxseed oil and quercetin have received extensive attention in food industry. However, their poor solubility in water and stability are major limitations for their application in functional foods. In this work, we encapsulated flaxseed oil and quercetin into submicron emulsions by high pressure homogenization method to overcome their shortcomings in application. The loading of flaxseed oil in submicron emulsions was 10% and the solubility of quercetin in water is increased by at least 1300 folds. In vitro antioxidant study indicated that the addition of flaxseed oil could increase the antioxidant activity of quercetin. During in vitro digestion, the smaller the particle size of submicron emulsions, the faster the digestive rate of flaxseed oil and the higher the bio‐accessibility of quercetin. Furthermore, accelerated oxidation study revealed that quercetin could protect flaxseed oil effectively. Besides, metallic ions stability study illustrated that the influence of Na+ on the emulsion stability is smaller than that of Ca2+ and high Ca2+ concentration could lead to stratification of the submicron emulsions. The storage stability shows that the prepared submicron emulsions can be stored for 8 weeks at three different temperatures. Hence, submicron emulsion can be a promising vehicle for delivery of flaxseed oil and quercetin.Practical Applications: Submicron emulsions can be used to improve the water solubility and bioavailability of lipophilic nutrients. The combination of flaxseed oil and quercetin in submicron emulsions can compensate for their individual shortcomings in application and exert synergistic beneficial actions on human health. Furthermore, this technology is easy in operation and can be realized in industry. Flaxseed oil and quercetin co‐loaded submicron emulsions can be applied in milk and liquid beverages in food industry.Submicron emulsions are fabricated to enhance the delivery of flaxseed oil and quercetin. The smaller the particle size of submicron emulsions, the faster the digestive rate of flaxseed oil and the higher the bio‐accessibility of quercetin. Quercetin can protect flaxseed oil against oxidation effectively. The antioxidant effect of quercetin is found to be better than commonly used antioxidants.