The invention relates to a preparation method of modified nano-silicon dioxide toughened epoxy resin; the preparation method comprises the following steps of: (1), adding 1-2g of amino silane coupling agent into 48-50g of absolute ethyl alcohol firstly, adding glacial acetic acid to adjust the pH (potential of hydrogen) value to be 3-4, shaking by ultrasonic wave in order to fully dissolve the amino silane coupling agent into the absolute ethyl alcohol; (2), putting 5-6g of nano-SiO2 into a flask, pouring 20-30g of the solution obtained in step (1), dispersing by ultrasonic wave for 30min, stirring for 3-5 hours at the constant temperature of 75 DEG C at the stirring speed of 450rpm, cooling, centrifugally separating, and drying for 24 hours at 140 DEG C, so as to obtain modified nano-silicon dioxide; and (3), adding 50-150g of liquid epoxy resin into a reaction container, heating to 60 DEG C, slowly adding 0.1-1% by weight of liquid epoxy resin of modified nano-silicon dioxide prepared by step (2) while stirring, after adding, stirring uniformly, dispersing by high-speed shearing, heating to 90 DEG C within 1 hour, and then reacting for 3-5 hours at a constant temperature, cooling, finally the product is obtained. The resin prepared by the preparation method is stable in property, and the property of the prepared coating is greatly improved.