Fischer−Tropsch synthesis, the conversion of CO and H 2 to long-chain hydrocarbons, is performed at relatively low temperatures and high pressures over the most commonly encountered iron-, ruthenium-, or cobalt-based catalysts. Identification of the morphologies and structure evolution of FTS catalysts under reaction conditions are essential for understanding the structure−reactivity relationship. In this work, we performed a comprehensive ab initio thermodynamics study to provide an understanding of the morphology evolution of cobalt (Co) catalyst with hexagonal close-packed (HCP) and face-centered cubic (FCC) crystal structures under a CO atmosphere. CO adsorption on numerous surfaces of HCP Co and FCC Co at different coverages were investigated. On both HCP Co and FCC Co, lateral interaction is attractive at lower coverage and becomes repulsive at higher coverage. Compared to FCC Co, though in average CO adsorption on HCP Co is stronger at lower coverage, they become similar at higher coverage due to the overwhelming lateral repulsion. We established the phase diagrams and the morphology evolution of FCC Co and HCP Co as a function of CO chemical potentials. The most probable exposed facets in FCC Co and HCP Co Wulff shapes were revealed under different CO atmospheres. At a relatively low CO chemical potential, many open facets could be exposed in Co equilibrium morphology, including {101̅ 2}, {101̅ 1}, {101̅ 0}, and {112̅ 0} facets for HCP Co and {311}, {110}, and {100} facets for FCC Co. In contrast, at a relatively high CO chemical potential, FCC Co has an octahedron shape composed entirely by close-packed {111} facets, while HCP Co is hexagonal prism shaped composed mainly by close-packed {0001} and {101̅ 0} facets. The morphology evolution of HCP and FCC phases would have great impact on the inherited catalytic performance of Co nanoparticles, thus will selectively regulate their chemical reactivity.