The present invention relates to the pharmaceutical synthesis field, and provides a method for synthesizing 5-isosorbide mononitrate by means of a micro-channel reactor. In the present invention, a nitrating reagent and isosorbide liquid are pumped into the micro-channel reactor respectively for mixing reaction; after the reaction is completed, a product flows out from an outlet of the micro-channel reactor, and is subjected to post-treatment, separation, and purification to obtain the target product 5-isosorbide mononitrate. According to the method provided in the present invention, reaction time is short, and compared with a conventional technology, the method is safe, and the yield of the 5-isosorbide mononitrate is greatly improved.