A method for preparing a high-quality epoxidized fatty acid ester with a micro-reaction device, including: respectively pumping an aqueous hydrogen peroxide solution and a carboxylic acid at the same time into a first micro-mixer; after the reaction in the first micro-reactor, respectively pumping the output material and an unsaturated fatty acid ester into a second micro-mixer;completely mixing them and then introducing the mixture into a second micro-reactor; and after a complete reaction, water-rinsing the organic phase part of the resultant reaction liquid and drying the same to obtain the epoxidized fatty acid ester.