The invention discloses a method for preparing epoxy fatty acid methyl ester by using a magnetic catalyst, which comprises the following steps of: reacting fatty acid methyl ester with a formic acid serving as raw materials under the catalysis of the magnetic catalyst in a way of adding dropwise hydrogen peroxide to produce a reaction product; separating and recycling the magnetic catalyst with amagnetic field; and standing, demixing, neutralizing and dehydrating the crude product to produce the epoxy fatty acid methyl ester product, wherein the magnetic catalyst is a core-shell type nanometer magnetic catalyst which has the inner core of Fe3O4, the hull of zirconium oxide, the structure of ZrO2/(SiO2-Fe3O4) and the particle size of 50 to 100nm. The method has the advantages of adopting a magnetic nano-size solid acid as the catalyst which has high activity and is easy to separate, avoiding corrosion, to equipment, of a sulfuric acid or an organic acid adopted as the catalyst in the conventional process, and reducing environmental pollution, along with high epoxy value, light color and high industrial application value.