Magnetite Fe₃O₄ (ferrite) has attracted considerable interest for its exceptional physical properties: It is predicted to be a semimetallic ferromagnetic with a high Curie temperature, it displays a metal-insulator transition, and has potential oxide-electronics applications. Here, we fabricate a high-magnetization (> 1 Tesla) high-resistance (~0.1 Ω·cm) sub-nanostructured (grain size < 3 nm) Fe₃O₄ film via grain-size control and nano-engineering. We report a new phenomenon of spin-flipping of the valence-spin tetrahedral Fe³⁺ in the sub-nanostructured Fe₃O₄ film, which produces the high magnetization. Using soft X-ray magnetic circular dichroism and soft X-ray absorption, both at the Fe L_{3, 2^-} and O K-edges, and supported by first-principles and charge-transfer multiple calculations, we observe an anomalous enhancement of double exchange, accompanied by a suppression of the superexchange interactions because of the spin-flipping mechanism via oxygen at the grain boundaries. Our result may open avenues for developing spin-manipulated giant magnetic Fe₃O₄-based compounds via nano-grain size control.