High-resolution transmission electron microscopy in conjunction with autocorrelation function analysis have been applied to investigate the evolution of structural order in germanium ion-implanted amorphous silicon (a-Si) layers. A high density of Si nanocrystallites as small as 1 nm in size was detected in as-implanted a-Si layers. The density of embedded nanocrystalline Si was found to diminish in a-Si layers with annealing temperature first then increase. The results are discussed in the context of free energy change with annealing temperature.