The invention discloses magnetic microsphere resin for removing nitrate nitrogen selectively, and a preparation method thereof, and belongs to the field of ion exchange resin. The resin consists of a resin skeleton, and magnetic granules wrapped in the resin skeleton; and the resin skeleton has a basic structural formula shown in the specification, wherein B is a quaternary ammonium salt group for adsorbing the nitrate nitrogen selectively, the saturation magnetization intensity of the quaternary ammonium salt group is between 5 and 30 emu / g, the exchange capacity of strong base is between 3.0 and 4.5 mmol / g, the exchange capacity of weak base is between 0.5 and 1.5 mmol / g, and the average grain diameter of the resin is between 50 and 500 micrometers. The resin is synthesized by a suspension polymerization method; acrylate monomers are mixed with a pore-forming agent and an initiator to form an oil phase; after being mixed with the magnetic granules uniformly, the mixture is subjectedto suspension polymerization with an aqueous phase mixed with a dispersing agent to form the magnetic polymer granules, and the magnetic polymer granules are subjected to aminolysis and alkylation toform the resin serving as a finished product. The resin can adsorb negative ions such as nitrates, nitrites and the like in a water body selectively, so the magnetic microsphere resin has a bright application prospect in fields of drinking water treatment, groundwater remediation and the advanced treatment of urban domestic sewage.