Medium-range order in ion-implanted amorphous silicon has been observed using fluctuation electron microscopy. In fluctuation electron microscopy, variance of dark-field image intensity contains the information of high-order atomic correlations, primarily in medium-range order length scale (1–3 nm). Thermal annealing greatly reduces the order and leaves a random network. It appears that the free energy change previously observed on relaxation may therefore be associated with randomization of the network. In this paper, we discuss the origin of the medium-range order during implantation, which can be interpreted as a paracrystalline state, that is, a disordered network enclosing compacts of highly topologically ordered grains on the length scale of 1–3 nm with significant strain fields.