The invention discloses a method for continuously preparing a 2-benzyl isoindolinone compound by adopting a microchannel reactor, which comprises the following steps: (1) respectively and simultaneously pumping a mixed solution containing 1,2-Benzenedimethanol, alcohol oxidase, flavin adenine dinucleotide and hydrogen peroxide reductase and air into a microchannel reaction device; carrying out a first reaction in a first microreactor containing nano MnO2; and (2) respectively and simultaneously pumping the first reaction effluent and a benzylamine compound solution into a second microreactor, and carrying out a second reaction to obtain the 2-benzyl isoindolinone compound as shown in a formula IV. The method has the advantages of short reaction time, high reaction conversion rate, few side reactions, small toxicity and pollution, low production cost, good product quality and the like, does not use noble metal catalysis in the reaction process, is green, environment-friendly, energy-saving and efficient, is suitable for popularization and application, and solves the problems of long reaction time, harsh reaction conditions and need of noble metal catalytic catalyst in the prior art.