We use fluctuation electron microscopy to characterize medium-range order in ion-implanted amorphous silicon. In fluctuation microscopy, intensity fluctuation in a dark-field image contains the information of high-order atomic correlations in the length scale of 1-3 nm. In this study, we heated as-implanted silicon at 500, 550, and 580 °C for various times. Our results indicate that in the beginning amorphous silicon is a disordered phase with robust medium-range order. Thermal annealing leads to disordering of the structure. Furthermore, we find that the activation energy of the disordering is about 2.7 eV, close to the activation energy for thermal relaxation (about 2.2 eV). Our finding suggests a strong correlation between structure disordering and thermal relaxation.