The present invention relates to an intermediate for preparing edoxaban free base and its preparation method and application. The preparation method of the intermediate comprises the following steps: in an organic solvent, under the action of a base, 5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c] Pyridine-2-carboxylic acid or its salt is reacted with acid chloride to obtain. Using the intermediate, the free base of edoxaban can be synthesized in a low-cost, green, environmentally friendly, simple, efficient and safe manner, and the drug safety of the obtained edoxaban product can be improved. The steps for preparing edoxaban free base are as follows: in an organic solvent, compound (II) and compound (IV) react to obtain; or, in an organic solvent, under the action of a base, compound (II) and compound ( IV) salt reaction, that is, obtained. The structures of compound (II), edoxaban free base, and compound (IV) are respectively as follows.