The invention discloses hydrophobic phosphogypsum, and a preparation method and application thereof. The hydrophobic phosphogypsum is prepared from phosphogypsum and a hydrophobic modifying agent. The preparation method comprises the following steps of: dissolving the hydrophobic modifying agent into solvent to produce the solution of the hydrophobic modifying agent; adding the phosphogypsum intothe solution; stirring the solution uniformly; reacting under a heating condition; pumping and filtering the solution when the solution is hot; and drying filter residue to obtain the hydrophobic phosphogypsum. The hydrophobic phosphogypsum can be used as inorganic filler applied to polymer. Compared with the prior art, the hydrophobic phosphogypsum has hydrophobic property due to the hydrophobicmodifying agent and is dispersed in the polymer highly and modifies the polymer by serving as the inorganic filler due to the hydrophobic property; the preparation method has the advantages of simpleness, easily-controlled technological parameters, readily available raw materials and low preparation cost; and the application way of the solid waste phosphogypsum is expanded and the modifying cost of the polymer is reduced.