Laser ablation of zircon can be used to analyze its composition for geological history. However, the effect of laser properties on nanoparticle size has not been studied extensively. The effect of laser fluence and pulse duration on the diameter of zircon nanoparticles was analyzed using field-emission scanning electron microscopy and energy dispersive spectroscopy. The results showed that the diameters of the zircon nanoparticles induced by a femtosecond laser increased with increasing laser fluence, and that these particles were smaller than those induced by a nanosecond laser with the same laser fluence. Furthermore, the mechanism of zircon nanoparticle formation induced by laser ablation has been discussed. The explosion mechanism is the primary mechanism of nanoparticle generation. In particular, the zircon nanoparticles induced by the femtosecond laser were the result of Coulomb explosion, while phase explosion contributed to the zircon nanoparticles induced by the nanosecond laser. Therefore, the nature of zircon nanoparticles induced by laser ablation is mainly determined by the pulse duration.