Bulk metallic glass (BMG) have attracted considerable attention during the last decades due to their excellent physical, chemical, and biomedical properties. This report aims to investigate the relationship between antibacterial performance, crystallization behavior and laser ablation parameters of Zr-based bulk metallic glass (Zr-BMG) after nanosecond laser irradiation. The surface morphology, crystallization behavior, surface quality, binding energy and Cu/Ni release properties were explored after laser irradiation. The formation of reactive oxygen species following the immersion of Zr-BMG in phosphate-buffered saline was evaluated using the 2’,7’-dichlorofluorescin diacetate method. Staphylococcus aureus was selected to assess the antibacterial performance of Zr-BMG and mouse osteoblasts were used to examine the in vitro cytotoxicity. The results showed that at a laser energy intensity lower than 0.08 J/mm2 the amorphous structure of Zr-BMG was retained after the irradiation process. Furthermore, the laser irradiation process considerably increased the antibacterial performance of Zr-BMG. The Cu/Ni release rate, reactive oxygen species concentration, and antibacterial properties were directly proportional to the laser energy intensity. However, surfaces with a high antibacterial rate also showed high cytotoxicity. The surface irradiated with 7 μJ ablation pulse and 200 mm/s irradiation speed showed a better balance between antibacterial and cytotoxic properties with amorphous status.