In this work, the segregation and structural transitions of CoNi clusters, between 1500 and 300 K, have been investigated using molecular dynamics simulations with the embedded atom method potential. The radial distribution function was used to analyze the segregation during the cooling processes. It is found that Co atoms segregate to the inside and Ni atoms preferably to the surface during the cooling processes, the Co[Formula: see text]Ni[Formula: see text] cluster becomes a core–shell structure. We discuss the structural transition according to the pair-correction function and pair-analysis technique, and finally the liquid Co[Formula: see text]Ni[Formula: see text] crystallizes into the coexistence of hcp and fcc structure at 300 K. At the same time, it is found that the frozen structure of CoNi cluster is strongly related to the Co concentration.