The invention discloses a preparation method of a graphene and two-dimensional noble metal cluster composite material, comprising following steps: oxidizing graphite in a solution to form graphite oxide, ultrasonically dispersing the graphite oxide in an aqueous solution to form a graphite oxide solution, and dropping the solution to the surface of a glass electrode before natural slow drying; dipping the glass electrode in a mixed solution containing ions of a mediate metal M (Pb or Cu) and noble metal ions, subjecting the glass electrode to underpotential deposition and dissolution and stripping in a certain potential interval, after multiple volt-ampere cycles, depositing a noble metal on the surface of a graphene layer in a two-dimensional cluster form, and forming the graphene and two-dimensional noble metal cluster composite material. The graphene and two-dimensional Pt/Ru cluster composite material prepared by the method has super-high catalytic activity for methanol oxidation reaction. The invention is expected to enrich the preparation methods of graphene composite materials, optimize their structure, improving their performance, and widen their applicable ranges.