The morphology evolution by thermal annealing induced dewetting of gold (Au) thin films on silicon (Si) substrates with a native oxide layer and its dependences on annealing temperature and atmosphere are investigated. Both dewetting degree of thin film and Au/Si interdiffusion extent are enhanced with the annealing temperature. Au/Si interdiffusion can be observed beyond 800 °C and Au-Si droplets form in both argon and oxygen (Ar + O2) and argon and hydrogen (Ar + H2) environments. In Ar + O2 case, the passive oxidation (Si + O2 → SiO2) of diffused Si happens and thick silicon oxide (SiOx) covering layers are formed. A high temperature of 1050 °C can even activate the outward growth of free-standing SiOx nanowires from droplets. Similarly, annealing at 800 °C under Ar + H2 situation also enables the slight Si passive oxidation, resulting in the formation of stripe-like SiOx areas. However, higher temperatures of 950-1050 °C in Ar + H2 environment initiate both the SiOx decomposition and the Si active oxidation (2Si + O2 → 2SiO(g)), and the formation of solid SiOx is absent, leading to the only formation of isolated Au-Si droplets at elevated temperatures and droplets evolve to particles presenting two contrasts due to the Au/Si phase separation upon cooling.