The invention discloses a preparation method of a selective water plugging agent and belongs to the technical field of high molecular materials. The preparation method comprises the following steps: mixing a pre-treated mixed solution and a silane coupling agent according to the mass ratio ranging from (80 to 1) to (100 to 1); adding modified graphene oxide which is 0.03 to 0.09 time of the mass of the pre-treated mixed solution, epoxidized soybean oil which is 0.01 to 0.02 time of the mass of the pre-treated mixed solution and a catalyst which is 0.008 to 0.009 time of the mass of the pre-treated mixed solution; after stirring and mixing, adding an initiator which is 0.01 to 0.03 time of the mass of the pre-treated mixed solution; after stirring and reacting, obtaining a blank mixture; filtering the blank mixture; and washing, drying and crushing to obtain the selective water plugging agent. The selective water plugging agent disclosed by the invention has excellent selective permeability and water plugging performance.