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In this paper, we fabricated graphene/Fe₃O₄ heterostructure devices by stacking monolayer graphene on magnetite (Fe₃O₄) substrate and investigated their magneto-transport properties. Interestingly, graphene/Fe₃O₄ heterostructure devices exhibit a giant magnetoresistance (MR) of 70% at a low magnetic field of 0.65T and at 11K, which is three times greater than that of graphene on SiO₂. Based on standard two-fluid model and LDA$+$U simulation, we showed that the observed enhanced MR effect is due to the increased disorder in graphene induced through the charge polarization via the alignment of C atoms of graphene over the charge ordered B-site cations of Fe₃O₄. Our results demonstrate a potential way to enhance graphene MR effect through coupling graphene with a suitable substrate with charge orbital ordering.