The optimization of structure-dependent activity of supported metal catalysts has driven the dynamic determination of the morphology of Co nanoparticles on ZrO2 using atomic-level simulations. Density functional theory (DFT) calculations combined with ab initio molecular dynamics (AIMD) simulations were used to investigate the surface structure, nucleation mechanism and morphology evolution of Con clusters supported on different ZrO2 facets. As the size of the Con (n = 1–5) cluster increases, the competition between Co-Co bonding and the interaction of Con clusters with the ZrO2 surface further promotes the nucleation of larger clusters. Co atoms prefer to nucleate into large clusters on both c-ZrO2(111) and t-ZrO2(101) surfaces, but this behavior is unfavorable on the m-ZrO2(-111) surface. The analysis of electric properties suggests that the types of hybrid orbitals and the number of electron transfer accounts for the difference in energies of Con clusters on ZrO2 surfaces. Further, the AIMD simulations verified the stable structure of small Co5 cluster obtained by DFT, and predicted the morphology of large Co13 clusters on ZrO2 surfaces under realistic reaction conditions, consistent with the experimental SAM images. Our work provides an intuitive understanding of structure and morphology evolution of catalysts for the targeted design of catalysts to achieve the desired activity and explore more reaction possibilities.