The invention discloses a micro reaction system and method for synthesizing 4-bromo-3-methylanisole through a two-phase method, and belongs to the technical field of chemical engineering. The micro reaction system comprises a micro mixer, a micro packed bed, a pipeline reactor and a liquid-liquid phase separator which are sequentially connected, an aqueous solution containing Br2 and HBr, and 3-methylanisole are used as raw materials, mixed in the micro mixer, and subjected to secondary crushing in the micro packed bed, bromination reaction is completed in the pipeline reactor, an organic phase is separated by the liquid-liquid phase separator, and then a target product is collected. By means of the system, the yield of the target product is significantly improved, and the system has the advantages of low energy consumption, high selectivity and continuous production.