The invention relates to a method for enriching vitamin K2 in natto bacillus fermentation liquid. The method comprises the following steps of step 1, performing centrifugation on the natto bacillus fermentation liquid, and collecting supernatant; step 2, adding a flocculant and a filter aid to the supernatant obtained in the step 1, then performing stirring, performing centrifugation, and collecting supernatant; step 3, adding Fe3O4@SiO2-G nanometer microspheres which are reduced to the supernatant obtained in the step 2, regulating the pH to 6.0-8.0, then performing stirring treatment under the condition of 20-35 DEG C for 10-30min, and then collecting magnetic materials after adsorption; and step 4, adding hexane to the magnetic materials after adsorption, performing ultrasonic parsing for 5-20min, then externally applying a magnet, collecting magnetic nanometer materials, pouring out organic phase, and performing filtering, wherein filtrate is a hexane solution rich in vitamin K2. According to the method for enriching vitamin K2 in natto bacillus fermentation liquid, the VK2 in the natto bacillus fermentation liquid can be quickly and efficiently enriched. The method has the advantages that the specific steps are simple, the materials are low in price, and can be reused, and the enrichment effect is efficient.