Abstract: Ghost pulses in free electron laser THz (FEL-THz) facility in CAEP are studied. The generation reasons and the impact of ghost pulses on the facility are analyzed. With electron dynamic simulation, thermal simulation, Monte Carlo simulation and prototype experiment discussion, the impact of ghost pulses is proved to include three aspects: the damage to interceptive measurement equipment, the thermal effects on the beam-line caused by beam wall loss, and higher radiation protection requirements. The results indicate that the ghost pulse is an important reason to limit the FEL-THz operation and should be eliminated. The method of eliminating ghost pulses is also discussed briefly.