To guide the experiment research, the thermal stability of composite silicon nanowire encapsulated in carbon nanotubes is investigated by computer simulation. The cubic-diamond-structured silicon nanowires with the same diameter and [111] orientationt are filled in some armchaired single-walled carbon nanotubes. The heat process of compound structure of silicon nanowire encapsulated in carbon nanotubes is simulated by classical molecular dynamic method. Through the visualization and energy analysis method, the thermal stability of composite structure is studied. The changes in the thermal stability of silicon nanowires and carbon nanotubes are explained by the relationship between carbon nanotube space constraint and van der Waals force. It is found that the diameter of the carbon nanotubes is closely related to the thermal stability of silicon nanowires inside. When the nanotube diameter is small, thermal stability of silicon nanowires increases; when the nanotube diameter increases up to a certain size, the thermal stability of silicon nanowires will suddenly drop significantly: until the distance between silicon nanowires and the wall of carbon nanotube is greater than 1 nm, the thermal stability of silicon nanowires will be restored. On the other hand, silicon nanowires filled into the carbon nanotubes have an effect of reducing the thermal stability of carbon nanotubes.