We report investigations of magnetoresistance (MR) in epitaxial and polycrystalline Fe3O4 films. MR in epitaxial Fe3O4 films exhibits a local maximum at TV and a large value of −20% at 60 K. Based on a 1D half infinite spin chain model, the fitting parameter, which depends on the volume fraction of electronic scattering boundaries, sharply increases below TV with the decreased temperature. We suppose that the twin boundaries formed below TV facilitate the increase in MR and can act as antiphase boundaries (APBs) where the magnetic moments across twin boundaries are coupled antiferromagnetically. Similar MR behavior in Fe3O4(100) and (111) epitaxial films manifests the independence of MR on the spatial distribution of APBs. The outline of normalized MR in the epitaxial films shows a distinct temperature dependence. The temperature dependence may result from the different electronic transport mechanisms in Fe3O4 films. In a polycrystalline Fe3O4 film, MR comes from the disordered distribution of magnetic moments at grain boundaries. The effects of APBs, twin boundaries, and grain boundaries on MR are discussed in detail.