The nucleation and thermal stability of Au, Ni, and Au–Ni nanoclusters on 6H-SiC(0001) carbon nanomesh as well as the interaction between Au–Ni bimetallic clusters and reactive gases have been studied by X-ray photoelectron spectroscopy (XPS) and scanning tunneling microscopy (STM). Both Au and Ni atoms grow as three-dimensional (3D) clusters. Annealing the Au/carbon nanomesh surface up to 1150 °C leads to complete desorption of the Au clusters, while interfacial reaction occurs between Ni clusters and the substrate surface when the Ni clusters are subjected to the same annealing process. The nucleation of Au–Ni clusters depends critically on the deposition sequence. Au atoms preferentially nucleate on the existing Ni clusters, leading to the formation of bimetallic clusters with Au enriched on the surface. If the deposition sequence is reversed, a part of Ni atoms nucleate between the Au clusters. The thermal stability of the Au–Ni clusters resembles that of the Ni/carbon nanomesh surface, irrespective of the deposition sequence. XPS characterization reveals that Ni atoms in Au–Ni bimetallic clusters are oxidized upon exposure to 5.0 × 10− 7 mbar O2 for 5 min at room temperature while negligible structure change can be detected when the bimetallic clusters are exposed to CO gas under the similar conditions.