Nano structured coating system demonstrates outstanding performance stemming from unique structure evolution. Zr/Si coating was proposed as an ideal candidate for the protection of Zr alloy cladding. However, the phase selection remains a challenge to coordinate the complex requirement under the service and accident conditions of reactor core. In this work, a phase selection mechanism for amorphous Zr-Si-O (abbr. ZSO) was elucidated by the competitive consumption of Zr layer by silicidation and oxidation, which was also scale-dependent. The energy-loss near-edge fine structure and nanoindentation were also employed to characterize the unique scale effect in the two processes. Both the oxides kinetics and elastic modulus gain indicated an immediate passivation process under the subcritical condition after the in situ phase selection of the amorphous ZSO. Ab initio molecular dynamics (AIMD) was performed to disclose the origination of depressed O migration in ZSO. The multilayer structure also shows accident tolerance potential. The interfacial phase selection provided a strategy to regulate mesoscale structure originating from nanomter interface and meets the diversified requirement for “structure-performance relationship” under the service and accident conditions.