Here, multi-scale observations by cryogenic-transmission electron microscopy (cryo-TEM) and advanced reactive-molecular dynamics (r-MD) simulations were used to understand the kinetic progression of Li nucleation. The cryo-TEM imaging revealed that amorphous metal deposits can be obtained at room temperature with very slow deposition rates, traditionally only possible with very high quenching rates (e.g. >106 K s-1) on Li nucleation and reveals the transition from amorphous disordered states to crystalline ordered ones as a function of current density and deposition time. The r-MD simulations provide additional understanding of the driving forces and kinetic pathways for the nucleation and the associated amorphous-to-crystalline (disorder-order or second-order) phase transition. The incubation time for the phase transition varies with the Li canonical ensemble size, mass and energy transfer rate between an ensemble and the neighboring ones, and as a function of current density (i.e. Li deposition rate). It is important to note that this is the first time the r-MD was used to simulate kinetic pathway in a discrete manner with canonical ensembles to assess the impacts from the kinetic regime, which is very different from the conventional temporal or spatial averaging methods according to the statistical thermodynamics. Although the r-MD results were developed independently from cryo-TEM experiments, i.e. without any empirical correlation; there is a high degree of agreement with experimental observations.