The effects of linearly polarized and circularly polarized femtosecond laser on the ablation threshold of ZrO2 and Al2O3 ceramics at different pulse numbers were investigated. The surface morphology of the ablated craters was analyzed by optical microscopy and scanning electron microscopy and the depth of the ablated craters was measured by laser scanning confocal microscopy. The results show that the saturation ablation threshold of the two materials at linearly polarized light is smaller than that of circularly polarized light. The saturation ablation threshold of ZrO2 is smaller than that of Al2O3 at the same polarization state. With the increase of pulse numbers, the surface structures of ZrO2 ablation craters develop from disorder to order, and periodic layer annular ripple structures and nanohole arrays are observed at linear and circular polarized light. Compared with linearly polarized light, the effect of circularly polarized light on the depth of ablated craters is stronger, and surface morphology is more sensitive to the change of laser fluence, at the same time, the periodic structures are more obvious.