Interlayer rotation and stacking were recently demonstrated as effective strategies for tuning physical properties of various two-dimensional materials. The latter strategy was mostly realized in heterostructures with continuously varied stacking orders, which obscure the revelation of the intrinsic role of a certain stacking order in its physical properties. Here, we introduce inversion-domain-boundaries into molecular-beam-epitaxy grown MoSe2 homobilayers, which induce uncommon fractional lattice translations to their surrounding domains, accounting for the observed diversity of large-area and uniform stacking sequences. Low-symmetry stacking orders were observed using scanning transmission electron microscopy and detailed geometries were identified by density functional theory. A linear relation was also revealed between interlayer distance and stacking energy. These stacking sequences yield various energy alignments between the valence states at the Γ and K points of the Brillouin zone, showing stacking-dependent bandgaps and valence band tail states in the measured scanning tunneling spectroscopy. These results may benefit the design of two-dimensional multilayers with manipulable stacking orders