Recently, significant advancements have been made in low-entropy Cu3Sn catalysts, showcasing their efficient catalytic CO oxidation capabilities. Hence, the atomic models of the Cu3Sn are worth established to further investigate their catalytic mechanisms. Here, the structural features and stability of (Cu3Sn)n clusters (n = 1–6) are investigated using the genetic algorithm combined with the density functional theory (DFT). The results reveal the structural evolution of these clusters from hollow cages to compact icosahedrons, where Cu atoms predominantly tend to grow together, while Sn atoms are dispersed at the edge positions. The Eb, Ef and Δ2E analyses show that the icosahedral (Cu3Sn)3 has a higher stability than that of its neighbors. The molecular dynamics simulations demonstrates its stability even at 1000 K. The molecular orbitals and density of states reveal that the (Cu3Sn)3 has an 1S21P61D102S21F1 superatomic electronic configuration. Electrostatic potential surfaces show that (Cu3Sn)n clusters have significant σ-hole regions at the Cu atomic sites, which can make the CO stretching frequency and bond length have a large red-shift. Moreover, the adsorption energy between the (Cu3Sn)3 and CO is the largest, reaching 1.17 eV. Our work provides inferences to the structural characteristics and adsorptions of the CuSn alloys at the atomic level.