In order to study the influence of general F-Theta lens on telecentric F-Theta lens on wafer marking process, a wafer laser marking system using 1 066 nm acousto-optic Q-switched pulse fiber laser as light source and general F-Theta lens and telecentric F-Theta lens respectively is built. Dot matrix marking is carried out on the wafer surface with the same process parameters, and the ablation threshold, defocus effect and ablation plan of wafers under two F-Theta lenses are studied. Moreover, the three-dimensional morphology of wafer identification area is analyzed by white light interferometer. It is found that general F-Theta lens and telecentric F-Theta lens have little effect on the ablation threshold of wafers. In terms of defocusing effect, the ablation aperture of ordinary F-Theta lens decreases gradually with the increase of defocusing amount, while the ablation aperture of telecentric F-Theta lens first increases and then decreases with the increase of defocusing amount. In terms of the mark quality in the marking range, the mark quality of the two in the center of the marking range is basically the same, the farther away from the center, the telocentric lens does not show better mark morphology.