This work applied the ultrasonic bonding to package flip chip GaN-based light emitting diodes (flip chip LEDs) on Si substrates. The effects of ultrasonic bonding parameters on the reliability of flip chip GaN-based LED were investigated. In the sequent aging tests, samples were driven with a constant current of 80 mA for hundreds hours at the room temperature. It was found that the electroluminescence (EL) intensity variation had a large correlation to the ultrasonic power, and then to the bonding temperature and force. A high bonding temperature and ultrasonic power and a proper bonding force improved the EL intensity significantly. It was contributed to a strong atom inter-diffusion forming a stable joint at the bonding interface, The temperature fluctuation in the aging test was the main factor to generate a high inner stress forming delamination at the interface between the chip and Au bump. As a result, delamination had retarded the photons to emit out of the LED packaging and decay its EL intensity.