The crystallographic shapes of nanocrystals play critical roles in determining their physical and chemical properties. Liquid phase synthesis serves as one of the most important approaches for preparing shape-controlled nanocrystals, therefore, understanding the formation mechanisms of the thermodynamic equilibrium structures of nanocrystals in liquid solution is important. Using in situ liquid cell transmission electron microscopy (TEM), we observe for the first time the shape transformation of individual palladium nanocrystals from energy unfavored spherical shapes into equilibrium truncated octahedrons in aqueous solution. Via quantitative analysis of the shape evolution dynamics of an individual Pd nanocrystal, we find that about 10% of nanocrystal atoms were relocated during the shape transformation. The mass transport is attributed to the synergetic effect of electron beam irradiation and water environment.