Ultrasonic bonding is the novel packaging method for flip-chip with high yield and low-temperature bonding. The bonding module is a core part of the bonding machine, which can transfer the ultrasonic energy into the bonding spot. In this paper, we propose topology optimization technique which can make new design of boding modules due to the constraints on resonance frequency and mode shapes. The designed bonding module using topology optimization was fabricated in order to evaluate the bonding performance and reliable operation during the continuous bonding process. The actual production models based on the proposed design satisfied the target frequency range and ultrasonic power. The bonding test was performed using flip-chip with lead-free Sn-based bumps, the results confirmed that the bonding strength was sufficient with the designed bonding modules. Also the performance degradation of the bonding module was not observed after the 300-hour continuous process with bonding conditions.