This work demonstrates a new strategy for controlling the evolution of twin defects in metal nanocrystals by simply following thermodynamic principles. With Ag nanocrystals supported on amorphous SiO2 as a typical example, we establish that twin defects can be rationally generated by equilibrating nanoparticles of different sizes through heating and then cooling. We validate that Ag nanocrystals with icosahedral, decahedral, and single‐crystal structures are favored at sizes below 7 nm, between 7 and 11 nm, and greater than 11 nm, respectively. This trend is then rationalized by computational studies based on density functional theory and molecular dynamics, which show that the excess free energy for the three equilibrium structures correlate strongly with particle size. This work not only highlights the importance of thermodynamic control but also adds another synthetic method to the ever‐expanding toolbox used for generating metal nanocrystals with desired properties.