The hydrogenated amorphous silicon (a-Si:H) film is the core structure of hetero junction with intrinsic thin layer solar cell. Its quality determinates the photoelectric conversion efficiency of this solar cell directly. The configuration of Si _yH _xis an important structure characteristic of a-Si:H films, and it can influence on the quality of a-Si:H thin films and their application properties. However, it is difficult to study them in depth and detail by the existing analytical and testing methods. In this paper, the structure configuration of Si _yH _xin a-Si:H /c-Si thin films and the effect of substrate temperature on its content have been simulated and analyzed by molecular dynamics method. A modified Tersoff potential developed by Murty was used to calculate the inter-atomic forces. The results showed that the Si _yH _xstructure in a-Si:H thin films can be summarized into six configurations. Three traditional configurations, including SiH, SiH ₂and SiH ₃, can be referred to as SiH _xconfigurations.The other three nove configurations, including HSi ₂(s), HSi ₂(l) and HSi ₃, can be referred to as HSi _yconfigurations. The main differences between the configurations of HSi ₂(l) and HSi ₂(s) are the longer Si—H bonds and bigger bond angle in HSi ₂(l) configuration than those in HSi ₂(s) configuration. All of the Si-H bonds in SiH _xconfigurations are strong chemical bonds, while the Si—H bonds in HSi _yconfigurations are weak physical bonds. The further calculations of the Si-H bond energies in six configurations have been carried out by the first principle method. According the bond energies results, we can deduce that the order of the stability of six configurations from high to low is SiH > SiH ₂> SiH ₃> HSi ₂(s) > HSi ₂(l) > HSi ₃. Comparing the Si—H bond energies of the six configurations with the solar energy, it is found that the Si-H bond energy in HSi _yconfiguration is in the range of visible and infrared light in solar light. Si—H physical bonds are easy to fracture in HSi _yconfiguration caused by solar light. This may be the main mechanism of producing Steabler-Wronski (S-W) effect in amorphous silicon thin film cells. In addition, the rise of substrate temperature in the deposition process of a-Si:H films will lead to a significant decrease in the configuration content of all kinds of Si _yH _xconfigurations.