Ion-beam deposition of amorphous Ge layers on different substrates (silicon and quartz) has been performed. Deposited amorphous Ge layers were subjected to pulsed laser annealing (λ = 0.69 μm, τ = 80 ns). Simultaneously the optical probing of the Ge surface was carried out. The computer simulation of heating processes and phase transitions was performed taking into account the temperature dependences of film and substrates’ parameters and phase transition energies. The results of the dynamics of heating, melting, crystallization and plasma formation processes are well described by simulation data. It is shown that the threshold values for radiation power density and phase transition rates are determined mainly by thermophysical parameters of the substrates and thermal contact between Ge melt and substrate.