The van der Waals stacking of Janus Ga2SeTe quadruple-atomic layers leads to the formation of polytype bulk crystals, where the stacking order plays a critical yet elusive role in their fundamental properties. Here, we perform first-principles density functional theory calculations to investigate the stacking-dependent structural, electronic, and vibrational properties of four Ga2SeTe polytypes. Our results indicate that the γ polytype has two sub-phases of γ [ABC] and γ [ACB]. Lattice vibration studies manifest that symmetry operations depend on the stacking orders, in which the irreducible representations of optically active modes at Γ for the β, ε, γ, and δ phases are Γ = 3A1 + 4B1 + 4E2 + 3E1, Γ = 7E+7A1, Γ = 11A1 + 11E, and Γ = 8E2 + 7E1 + 8B1 + 7A1, respectively. Moreover, taking spin–orbit coupling into account, the estimated indirect bandgaps are 0.967, 0.926, 0.879, 0.925, and 0.950 eV for β, ε, γ [ABC], γ [ACB], and δ polytypes, respectively, in which the bandgap differences between indirect and direct transitions are within 10 meV. The Bader charge analysis indicates that the stacking order modulates the charge distribution among the compositional layers. These findings provide valuable insights for the development of optoelectronic devices based on Janus structures.