The invention belongs to the technical field of a nano material, and particularly relates to a ferrate magnetic nanocomposite with a core-shell structure, and a preparation method thereof. The magnetic nanocomposite is applied to a magnetic resonance imaging contrast agent; the nanocomposite takes CoFe2O4 as a core; a ferrate shell layer is wrapped at the surface; and the particle size of the material is 5-20nm. The preparation method comprises the steps of dissolving diacetone zinc/manganese and diacetone iron into an organic solvent; ultrasonically mixing and then adding CoFe2O4 nano particles and 1,2-hexadecanediol; magnetically stirring to obtain a mixed solution; heating the mixed solution under the inert gas atmosphere, cooling reaction liquid; adding absolute ethyl alcohol to the reaction liquid and carrying out centrifugal separation, freezing and drying to obtain a sample. The nano material is even in particle size, good in water-solubility, small in toxic and side effects, good in imaging effect, simple in preparation process of the material, and strong in reaction controllability, and can be used as a T2 contrast agent in magnetic resonance imaging detection.