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_x is 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_x in 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_x structure in a-Si:H thin films can be summarized into six configurations. Three traditional configurations, including SiH, SiH₂ and SiH₃, can be referred to as SiH_x configurations.The other three nove configurations, including HSi₂(s), HSi₂(l) and HSi₃, can be referred to as HSi_y configurations. The main differences between the configurations of HSi₂(l) and HSi₂(s) are the longer Si—H bonds and bigger bond angle in HSi₂(l) configuration than those in HSi₂(s) configuration. All of the Si-H bonds in SiH_x configurations 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_y configuration is in the range of visible and infrared light in solar light. Si—H physical bonds are easy to fracture in HSi_y configuration 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.