An understanding of nanocrystal shape evolution is significant for the design, synthesis, and applications of nanocrystals with surface-enhanced properties such as catalysis or plasmonics. Surface adsorbates that are selectively attached to certain facets may strongly affect the atomic pathways of nanocrystal shape development. However, it is a great challenge to directly observe such dynamic processes in situ with a high spatial resolution. Here, we report the anomalous shape evolution of Ag₂O₂ nanocrystals modulated by the surface adsorbates of Ag clusters during electron beam etching, which is revealed through in situ transmission electron microscopy (TEM). In contrast to the Ag₂O₂ nanocrystals without adsorbates, which display the near-equilibrium shape throughout the etching process, Ag₂O₂ nanocrystals with Ag surface adsorbates show distinct facet development during etching by electron beam irradiation. Three stages of shape changes are observed: a sphere-to-a cube transformation, side etching of a cuboid, and bottom etching underneath the surface adsorbates. We find that the Ag adsorbates modify the Ag₂O₂ nanocrystal surface configuration by selectively capping the junction between two neighboring facets. They prevent the edge atoms from being etched away and block the diffusion path of surface atoms. Our findings provide critical insights into the modulatory function of surface adsorbates on the shape control of nanocrystals.