In the gear transmission system, up to 60% of the faults are caused by gears, and their status directly determines whether the equipment can operate safely. Most of the research on equipment fault diagnosis and life prediction is carried out by analyzing dynamic response, but it takes a lot of manpower, material resources and time cost to obtain vibration response data through experiments. Aiming at the problem of different working conditions of gear transmission system and the scarcity of fault data samples, it is of great significance to develop its digital twin system. The digital twin system can not only display the running state of the gear transmission system in real time, but also generate high-quality vibration signals of the gear transmission system under different working conditions and faults through dynamic simulation signals and measured signals. In this paper, a rigid-flexible coupling multi-body dynamics model of fatigue test gear transmission system is established, and a digital twin system of fatigue test gear transmission system driven by digital and analog is developed. It can realize the simulation signal instead of the measured signal, which greatly saves the experimental cost and effectively supports the fault diagnosis and intelligent operation and maintenance of parallel shaft spur gear transmission system under few samples.