Au nanoparticles with a mean diameter of 20 nm with a coverage of ∼20% of the surface were distributed on a Si wafer surface and studied both before and after being annealed (at 100 and 300 °C). The two types of samples were analyzed using secondary ion mass spectroscopy (SIMS) with Bi₃⁺ clusters as the primary ions combined with surface etching using Ar₁₀₀₀⁺ clusters. We observed a substantial difference in the SIMS spectra combined with a relatively short sputtering time of Ar₁₀₀₀⁺. In the nonannealed samples, bare Au cluster cations and Si⁺ were observed in the SIMS spectra; AuSi⁺ clusters were also observed in the annealed samples. These results indicate Au-silicide formation at a part of the periphery of the Au nanoparticles upon annealing. We suggest that SIMS experiments using cluster ions such as Bi₃⁺ can not only be used for surface elemental analyses but also provide information on local chemical environments of elements on the surface. This is an important issue in heterogeneous catalysis (e.g., strong metal–support interactions). We also advise that one should be careful interpreting the SIMS data combined with a longer Ar₁₀₀₀⁺ sputtering time because this can deteriorate the surfaces from their original structures.