The invention relates to a preparation method of a magnetic iron-based heterogeneous Fenton catalyst taking graphene as a carrier and an application. According to the method, the graphene serves as the carrier, magnetic nano-scale ferroferric oxide and nano-scale zero-valent iron (Fe0) are compounded to the surface of the graphene to serve as the heterogeneous Fenton catalyst in an in-situ growth mode, aggregation of catalytic active nano-particles can be effectively prevented by the graphene serving as the carrier, and more active sites are exposed. Besides, the graphene has high electron transfer capability, Fe0 easily transfers electrons to Fe3+ by taking the graphene as the carrier, Fe3+ is promoted to be transformed into Fe2+, so that catalytic activity of the catalyst is improved, the catalyst is easily recovered and reusable, pollutant removal efficiency is improved, phenol removal efficiency reaches 99% or more, and the used catalyst is recovered by an external magnetic field. The preparation method solves the problems that traditional Fenton catalysts are difficultly recycled and generate a lot of chemical sludge, and the preparation method has a certain economic value and practical value.