A novel method of error analysis for opto-mechanical system by considering issues of the space and time stability is proposed. According to the theory of error transfer model and the system stability requirements, the temporal parameter is introduced as the dynamic compensate to reflect the structure random response influencing the position precision in the period of working time. The error transfer model originated from our method is also put forward. Moreover, the simulation is used to analyze the error of spatial filter system in Shenguang (SG) II facility. The results show that the method can more effectively deal with the target position error induced by the system structure, and it also provides a dynamic error analysis method for the high power laser facility and other great science projects.