Owing to the stimulus-responsive and dynamic properties, magnetism-driven assembly of building blocks to form ordered structures is always a marvelous topic. While abundant magnetic assemblies have been developed in ideal physical and chemical conditions, it remains a challenge to realize magnetic assembly in complicated biological systems. Herein, we report a kind of biomacromolecule-modified magnetic nanosheets, which are mainly composed of superparamagnetic graphene oxide (γ-Fe2O3@GO), the tumor-targeting protein transferrin (TF), and the mitochondrion-targeting peptide (MitP). Such large-size nanosheets (0.5–1 μm), noted as L-Fe2O3@GO-MitP-TF, can successfully in situ assemble on the surface of tumor cells in a size-dependent and tumor cell-specific way, leading to severe inhibition of nutrient uptake for the tumor cells. More significantly, the nanostructures could efficiently confine the tumor cells, preventing both invasion and metastasis of tumor cells both in vitro and in vivo. Moreover, the 2D assemblies could remarkably disrupt the mitochondria and induce apoptosis, remarkably eradicating tumors under near-infrared (NIR) irradiation. This study sheds light on the development of new nano-systems for efficient cancer therapy and other biomedical applications.