The experimental shape control of metallic Co nanoparticles (NPs) remains a great challenge in terms of their direct characterization for the further rational design and optimization of efficient nanocatalysts nowadays, especially when a low promoter content is involved. Thus, spin-polarized density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations have been carried out to investigate the adsorption configurations and growth trend of Ru_n clusters on Co surfaces to systemically explore the surface morphology of Co NPs induced by Ru promotion in Co-based Fischer–Tropsch synthesis (FTS). The predicted Ru_n aggregation adsorption patterns on Co(100) and Co(110) surfaces combined with the recent results for Co(111) and Co(311) surfaces show the thermodynamic growth tendency that Ru_n aggregates are favorable for planar layered growth on Co surfaces under realistic FTS reaction conditions, which is consistent with the experimental EELS spectral results. The addition of Ru promoter has an important role in tuning the stability of the exposed facets of face-centered-cubic (FCC) Co NPs, accompanied by the change from truncated octahedron to rhombic dodecahedron morphology. At high Ru content, the increased high index Co(311) and Co(110) surfaces, including more active step and kink sites, are desirable for the enhanced activity of FCC Co NPs.