A laser drilling system for flexible printed circuit board includes a first mirror, a second mirror, a laser crystal, a third harmonic generator and a second harmonic generator. The first mirror and the second mirror are spaced apart and defined a resonator cavity therebetween. The laser crystal is disposed in the resonator cavity for generating a fundamental laser beam. The third harmonic generator and the second harmonic generator are disposed the resonator cavity. A fundamental laser beam is directed to the second harmonic generator for generating a second harmonic laser beam, the fundamental laser beam and the second laser harmonic laser beam is directed to the third harmonic generator for generating a third harmonic laser beam, the third harmonic laser beam is output from the resonator cavity. A laser drilling method for flexible printed circuit board is also provided.