High-efficiency and high-quality sterilization technologies for medical materials can significantly reduce iatrogenic infection. This study investigates the synergistic effects of laser-induced periodic surface structures (LIPSS) and ultrasonic cleaning on the removal of bacteria from medical material surfaces. We specifically examined how ultrasonic parameters and structural defects in LIPSS impact the effectiveness of bacterial removal. As an emerging medical metal, Zr-BMG was chosen for the target material. Femtosecond laser processing was employed to create LIPSS with both complete linear arrays and discontinuous linear arrays structures featuring surface defects by adjusting the scanning overlap rate. A high-concentration solution of S. aureus was used for co-cultivation, resulting in a surface bacterial coverage rate exceeding 95%. The study analyzed the synergistic sterilization effect of microstructured surfaces through variations in ultrasonic cleaning power and duration. The results indicated that surfaces with microstructures demonstrated significantly improved bacterial removal following ultrasonic cleaning. The bacterial removal rate was found to be proportional to the ultrasonic vibrator power, and the surface with a LIPSS structure outperformed the discontinuous LIPSS surface in bacterial removal efficiency. Optimal results were achieved with the LIPSS surface after 30 min of cleaning at 100 W ultrasonic power. However, there was minimal difference in bacterial removal between 10 and 30 min at the same power level. This study aims to provide methodological insights and data support for the efficient and high-quality cleaning of medical metal surfaces.