Flip-chip bonding is a kind of chip packaging technology, which can make fabricated chips lighter and smaller. Thermo-ultrasonic flip-chip bonding is a technology that directly joins gold pad and gold bump. This study combines principle component analysis and gray relational analysis to determine the optimal processing parameters for multiple quality characteristics of light emitting diodes (LEDs). The quality characteristics of this experiment include the candle light, forward voltage, and leakage current of LED and thrust value. First, this study determines the processing parameters that may affect the thermo-ultrasonic flip-chip bonding with the L18 orthogonal array, including substrate temperature, bonding downforce, ultrasonic working time, ultrasonic power, and rising and delay time of tool head bonding. Then, the gray relational analysis is applied to indicate the optimal processing parameters for the multiple quality characteristics of LED. Since the Taguchi method only takes one single quality characteristic into consideration, this study applies the Taguchi method to reduce the number of thermo-ultrasonic flip-chip bonding experiments. The experimental results prove that the optimal LED has good integral quality, which is above industrial standard.