Atomic segregation in bimetallic clusters can influence the surface nucleation and also the structures of clusters. It is important to study the effect of atomic segregation on the structure. In this study, initial cooling temperatures were used to tune the atomic segregation ability. Molecular dynamics simulation with an embedded atom method was used to study the relationship between the structure and atomic segregation. It was found that the higher the initial cooling temperature, the more obvious the Ag atomic segregation. When the clusters cooled down from 800 K and 600 K, the clusters formed a mixed icosahedron due to the weak atomic segregation ability. When the initial cooling temperature is higher than 1200 K, all the Ag atoms segregated to the surface layer, the clusters formed a Pd – Ag -core–shell chemical ordering. For 1200 K initial temperature, the structure is decahedral. The clusters formed an fcc structure when the clusters cooled down from 2000 K, 1800 K, and 1500 K. When the clusters cooled down from 860 K and 900 K, not all the Ag atoms segregated to the surface layer, the clusters formed a core–shell chemical ordering with a mixed Pd – Ag core. But the structure of 860 K is twinned of icosahedron and decahedron and that of 900 K is decahedral. This means that the chemical orderings and structures were influenced by the atomic segregation.