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Abstract Despite the large number of reports on colloidal nanocrystals, very little is known about the mechanistic details in terms of nucleation and growth at the atomistic level. Taking bimetallic core-shell nanocrystals as an example, here we integrate in situ liquid-cell transmission electron microscopy with first-principles calculations to shed light on the atomistic details involved in the nucleation and growth of Pt on Pd cubic seeds. We elucidate the roles played by key synthesis parameters, including capping agent and precursor concentration, in controlling the nucleation site, diffusion path, and growth pattern of the Pt atoms. When the faces of a cubic seed are capped by Br − , Pt atoms preferentially nucleate from corners and then diffuse to edges and faces for the creation of a uniform shell. The diffusion does not occur until the Pt deposited at the corner has reached a threshold thickness. At a high concentration of the precursor, self-nucleation takes place and the Pt clusters then randomly attach to the surface of a seed for the formation of a non-uniform shell. These atomistic insights offer a general guideline for the rational synthesis of nanocrystals with diverse compositions, structures, shapes, and related properties.