A class-D amplifier and a method of generating a multi-level output signal thereof are provided. The class-D amplifier includes a controlling logic circuit and an output module. The controlling logic circuit analyzes the amplitude of an input signal to generate a voltage modifying signal. A power supply provides a voltage according to the voltage modifying signal. The controlling logic circuit generates controlling signals according to the input signal. The output module generates an output signal to drive a load according to the voltage and the controlling signals. In other words, the resolution of the amplitude of the output signal is increased by modifying the voltage, and a signal to noise ratio is then increased.