The invention discloses a molecular cluster material of supramolecular polymer and a preparation method and application of the molecular cluster material. The preparation method includes the steps of firstly, preparing polystyrene microspheres; secondly, using polystyrene microspheres as the substrates, and grafting active groups containing a large amount of carboxyl or sulfonic group to the surfaces of the polystyrene microspheres so as to synthesize the molecular cluster material. The preparation method has the advantages that the method is simple, low in cost, low in energy consumption, environmentally friendly and free of pollution; the prepared molecular cluster material is efficient, stable, large in descaling amount, high in oxidation resistance, high in mechanical strength, easy in large-scale production and applicable to water scale removing of drinking water. The molecular cluster material has the advantages that crystal chemistry and hydromechanics are powerfully combined, and the molecular cluster material mainly uses physical descaling and is stable in descaling performance and capable of achieving automatic regeneration; the molecular cluster material is large in treatment capacity and wide in application range, and the effect of the molecular cluster material is more than 3 times of that of descaling using softened resin; the molecular cluster material is high in discharge water quality, and raw water hardness after treatment can reach an international standard.