The passivation interfaces of GaN-based MIS-HEMTs with Si3N4 and ZrO2/Si3N4 bilayers were investigated through atomic resolution scanning transmission electron microscope–energy dispersive spectroscopy–differential phase contrast microscopy methods. It is found that the Si3N4/GaN interface exhibits atomic disorder fluctuation, and the GaN surface is discontinuous at the depth of 1–2 atomic layers. An oxide layer of ∼2 nm is formed at the ZrO2/GaN interface, and the GaN surface is atomically flat. Furthermore, the local minimum of the potential is located at the Si3N4/GaN interface, while it is distributed in the GaN side at the ZrO2/GaN interface. The electric field or potential distribution is affected by the crystal orientation of the polycrystalline ZrO2 layer. Finally, the difference in passivation mechanism is discussed.