We describe the first investigation into the influence of the crystal structure of AuRu3 alloy nanoparticles (NPs) on their thermal stability and catalytic properties. The hexagonal close-packed (hcp)-AuRu3 alloy NPs show better thermal stability than the face-centered cubic (fcc)-AuRu3 alloy NPs. The difference in catalytic properties was investigated through the oxygen evolution reaction. Both fcc- and hcp-AuRu3 alloy NPs show onset potentials comparable to Ru NPs. However, the hcp alloy NPs show higher durability than the fcc alloy NPs.