Silicon-contained coatings are rarely used on Zr alloy cladding tubes, mainly because the continuous SiO4 tetrahedral structure is easy to be destroyed in subcritical environment. Based on the continuous mixing structure of SiOx tetrahedron and ZrOx polyhedron, amorphous Zr–Si–O (ZSO) coating was proposed in this work. The key to the long-term protection of ZSO coating lies in the bonding status and structural stability under working conditions. According to first-principle calculation and atomic bonding characterization, the stable mechanism of amorphous ZSO coating was established, from the point of elemental diffusion and the stability of two interfaces (Zr/ZSO, ZSO/H2O). Based on the regulation of atomic bonding and packing condition, a trade-off of “diffusion barrier” and “hydrochemical stability” was designed in the optimized ZrSi3O coating experimentally. All the elements were in a strong hybrid bonding state, which ensures the stability of atomic structure and long-term protection performance. The results of the 400 ℃ air environment oxidation experiment show that the Zr–O–Si coating can provide good protection for Zr alloys. When subjected to air burning oxidation at 600 and 800 ℃, the coating still provides protection to the Zr alloy, but microcracks begin to appear on the surface of the coating.