A multi-channel digital amplifier system to generate a pulse width modulation (PWM) signal having a different switching frequency in each channel, and a signal processing method thereof. The digital amplifier system includes a PWM conversion unit to convert a plurality of audio signals on a plurality of channels into low output power PWM signals having switching frequencies that are different from each other, a switching circuit unit to amplify the plurality of low output power PWM signals to a plurality of high power output PWM signals on the respective channels, and a filter unit to restore the plurality of high output power PWM signals to a plurality of analog audio signals on the respective channels.