Cellulose nanofibril (CNF) has become a renewable and sustainable building block for functional and structural materials. In this study, combining chemical structure analyses, mechanical experiments, and first principle calculations, we elaborate on the strengthening and toughening mechanisms for the wet-drawn bacterial cellulose (BC) films that contain metal ion crosslinks. Wet-drawing assists the alignment of CNFs, and multivalent metal ion cross-linking further improves the inter-fibril interactions. BC films cross-linked with Na+, Ca2+, Cu2+, Al3+, and Fe3+ all demonstrate improved mechanical strength than the as-received samples. Density functional theory (DFT) calculations reveal that besides the electrostatic forces between the metal ions and the adjacent carboxylate oxygen atoms, Cu2+ and Fe3+ can also form coordination bonds with the adjacent carboxylate oxygen atoms. Among all the five metal ions tried herein, Fe3+ introduces the strongest cross-links between nanofibrils through coordination bonds and electrostatic forces. The BC films cross-linked with Fe3+ exhibit high tensile strength and toughness of 451.51 MPa and 8.19 MJ∙m−3, respectively. The underlying mechanisms discovered herein open new possibilities for utilizing natural fibers.