The invention discloses a composite polyethyleneimine-modified graphene oxide compound material, and a preparation method and an application thereof. The compound material comprises graphene oxide, low molecular polyethyleneimine, macromolecular polyethyleneimine and a cross-linking agent, wherein the low molecular polyethyleneimine and the macromolecular polyethyleneimine are modified on the surface of the graphene oxide through the cross-linking agent; the macromolecular polyethyleneimine is the polyethyleneimine of which the relative molecular weight is greater than or equal to 20,000; and the low molecular polyethyleneimine is the polyethyleneimine of which the relative molecular weight is smaller than 5,000. The preparation method comprises the steps of dispersing the graphene oxide into water and adding the cross-linking agent to prepare a suspension; mixing the macromolecular polyethyleneimine and the low molecular polyethyleneimine, adding the cross-linking agent to prepare a mixed solution; and dropwise adding the mixed solution to the suspension, stirring and dialyzing by using a dialysis bag. The composite polyethyleneimine-modified graphene oxide compound material is high in transfection efficiency and low in toxicity, can be applied to gene transfection and drug delivery, and has the advantages of being efficient, fast and safe.