The relationship between the local structures and the thermodynamic properties of metallic liquids has been a fundamental issue, which significantly impacts the comprehensive performances of metallic materials. The temperature-induced structure evolution in CoxBy alloy liquids, involving CoB, Co2B, Co3B, and Co23B6, was investigated using ab initio molecular dynamics simulations. The results show that the clusters of icosahedral-like polyhedrons are found predominantly in all alloys at low temperature, while the heating induces the decrease in ideal icosahedral and the increase in defected icosahedral. At high temperature, the polyhedron clusters decrease significantly and the ideal icosahedra transforms into smaller short-range polyhedrons, signifying the temperature-induced chemical structure change from long-range to short-range ordering. The aggregation of B atoms at high temperature is confirmed by atomic configuration, charge density, and B-centered Voronoi polyhedrons, and the α-Co single phase is observed below 1600 K. This study is helpful for understanding the local structure variability in eutectic Co-B alloys and guiding solidification path in theory.