In this work, SRO thin films were prepared by magnetron sputtering and converted to Si nano-crystals (Si-NCs) by rapid thermal annealing (RTA). Further tube-furnace annealing was performed on the Si-NC films in order to reduce residual stress. The residual stress in the Si-NC thin films after RTA at 1100 and 1200 °C were determined as 2.41 and 1.87 GPa, respectively, and the following tube-furnace annealing can obviously decrease the residual stress. The residual stress decreased with increasing annealing temperature and time. The following tube-furnace annealing at 1100 °C for 60 min and 1000 °C for 180 min reduced the residual stress to 1.46 and 1 GPa, respectively, for the Si-NC thin films with prior RTA at 1200 °C. The reduction of residual stress was ascribed to the larger density of extended defects and the lower surface-to-volume ratio of the thin films.