The invention relates to a composite magnetic cation exchange resin, as well as a preparation method and application thereof. The resin consists of macroporous cation exchange resin at an outer layer and one or a plurality of magnetic cores embedded inside, wherein the weight ratio of the macroporous cation exchange resin to the magnetic cores is 0.4-10:1; each magnetic core consists of gel-type resin and one or a plurality of magnetic particles embedded inside the gel-type resin; and the weight ratio of the gel-type resin to the magnetic particles is 1.2-100:1. The preparation method comprises the steps of coating the magnetic particles with the gel-type resin so as to prepare the magnetic cores, coating the outer layers of the magnetic cores with the macroporous resin, performing sulfonation or hydrolysis and obtaining the composite magnetic cation exchange resin. The composite magnetic cation exchange resin provided by the invention can be used in metal enrichment, wastewater treatment, biochemical, medical, pharmaceutical and other fields, and particularly the composite magnetic strong-acidic resin provided by the invention can be used for catalytic polymerization, etherification, hydration and other chemical reaction in magnetically stabilized beds, magnetically fluidized beds, magnetic suspension beds and other reactors.