Lithium metal has been considered an ideal anode for high-energy rechargeable Li batteries, although its nucleation and growth process remains mysterious, especially at the nanoscale. Here, cryogenic transmission electron microscopy was used to reveal the evolving nanostructure of Li metal deposits at various transient states in the nucleation and growth process, in which a disorder–order phase transition was observed as a function of current density and deposition time. The atomic interaction over wide spatial and temporal scales was depicted by reactive molecular dynamics simulations to assist in understanding the kinetics. Compared to crystalline Li, glassy Li outperforms in electrochemical reversibility, and it has a desired structure for high-energy rechargeable Li batteries. Our findings correlate the crystallinity of the nuclei with the subsequent growth of the nanostructure and morphology, and provide strategies to control and shape the mesostructure of Li metal to achieve high performance in rechargeable Li batteries.