Based on the vibration characteristics of gas turbine rotor rubbing fault, the dynamic equation of the 9F stage gas turbine rotor is established, and the temperature factor is introduced into the equation. Secondly, structure model of 9F gas turbine rotor is built. Then, the transient thermal stress analysis of the rotor is carried out, meanwhile, considering the influence of thermal-structure coupling. The temperature field and thermal stress of rotor from normal operation to 72 hours of shutdown are studied. The analysis results show that the application of finite element analysis method to study the vibration characteristics of the 9F gas turbine rotor is feasible. Furthermore, the effect of the rotor thermal-structure coupling is taken into consideration, and it is of great significance to study the vibration characteristics of rotor rubbing fault more accurately.