The invention relates to a nano-emulsion simultaneously loaded with linseed oil and lutein and a preparation method thereof, and the nano-emulsion is prepared from the following raw materials in percentage by mass: 0.4%-1% of lutein, 4%-10% of linseed oil, 0.8%-1.5% of linseed gum, 3%-6% of glycerol, 5%-10% of medium chain triglyceride and the balance of ultrapure water. The preparation method comprises the following steps: stirring and dissolving lutein, linseed oil, glycerol and medium chain triglyceride to obtain an oil phase, stirring and dissolving linseed gum and water to obtain a water phase, pouring the water phase into the oil phase, continuously stirring to be uniform, and carrying out ultrasonic emulsification or high-pressure homogenization to obtain the nano emulsion compounded with linseed oil and lutein. The linseed oil and the xanthophyll are creatively loaded in the nano-emulsion at the same time, so that the solubility of the linseed oil and the xanthophyll in a water-based matrix is improved, and the stability and the bioavailability of the linseed oil and the xanthophyll are remarkably improved. The nano-emulsion has good regulation and protection effects on a large number of groups using eyes, and is an ideal functional product.