The present invention relates to a method of preparing methyl tert-butyl ether including a reaction step of reacting methanol with iso-butene in the presence of an acid catalyst to generate methyl tert-butyl ether; and a purification step of purify the reaction product obtained by the reaction step by introducing the reaction product into a reaction distillation column including a packing stage containing an acid catalyst, wherein a flow ratio of a recycle to a fresh feed is different per the volume of each reactor. Accordingly, the amount of unreacted iso-butene and the amount of impurities included in the reactor may be reduced, resulting in reduction of the amount of thermal energy used in a reaction distillation column. [Representative Figure] FIG. 1