We have studied the surface atomic configurations around antiphase domain boundaries (APBs) in epitaxial magnetite (Fe3O4) thin films on MgO(001) by scanning tunneling microscopy (STM). The observed surface of the Fe3O4 films is the B-plane terminating surface with the (√2×√2)R45° reconstruction. Several variations of APBs are observed by STM at atomic resolution. The observed APBs are categorized into a APBs labeled by three different phase shift vectors: in-plane 1/4[110], in-plane 1/2[100], and out-of-plane 1/4[101]. We discussed how these APBs appear on the surface. The proportions of the APBs with 1/4[110], 1/2[100], and 1/4[101] shifts are about 38, 1, and 61%, respectively, in our experiment.