Laser cleaning technology, which is environment-friendly, has a wide range of application prospects in remanufacturing, micro-electro-mechanical system (MEMS) and ultra-precision machining. The mechanism and experimental research of removing paint layer from FV520B substrate with low frequency pulsed YAG laser is carried out. The experimental results show that, the removal mechanism differs under different experimental conditions, which is mainly ablation effect when blowing argon but transfers into vibration effect and ablation effect when water as a transparency overlay is used. The overlay water can not only increase the removal rate but also enlarge the damage threshold of laser. The removing effect of overlapping ratio is also calculated, that is, with the laser scanning speed of 249 mm/min and the overlap value between two traces of 0.6 mm, the whole paint layer can be removed completely with the removal rate of 15.5 mm2/s.