Spinel-type magnetite Fe3O4 is predicted to be a half-metal material with negative spin polarization. However, magnetic tunnel junctions (MTJs) using an Fe3O4 electrode exhibit a small tunnel magnetoresistance (TMR) effect, the sign of which has not been established experimentally. The development of Fe3O4 as an excellent TMR material requires a better understanding of the characteristics of the interface and the phase transition of Fe3O4 called the Verwey transition. We fabricate MTJs using epitaxial Fe3O4-based stacks on MgO(001) substrates and find a large inverse TMR ratio of -55.8% at 80 K, which corresponds to 126% by the optimistic definition of the TMR ratio. The temperature dependence of the TMR ratio is significantly affected by the Verwey transition. Moreover, we investigate the dependence of TMR on oxygen partial pressure during Fe3O4 deposition. It is found that the magneto-transport properties of the MTJs show different behaviors depending on the oxygen partial pressure because the Verwey transition is sensitive to the oxygen concentration. Furthermore, the electronic and magnetic properties at the interfacial regions are investigated by x-ray magnetic spectroscopy and first-principles calculation. These findings greatly support the use of Fe3O4 in spintronic devices and should lead to further developments in oxide spintronics.