A method for cleaning semiconductor substrate (1010,2010) without damaging patterned structure on the semiconductor substrate (1010,2010) using ultra/mega sonic device (1003,2003) comprises applying liquid into a space between a substrate (1010,2010) and an ultra/mega sonic device (1003,2003); setting an ultra/mega sonic power supply at frequency f1 and power P1 to drive the ultra/mega sonic device (1003,2003); before bubble cavitation in the liquid damaging patterned structure on the substrate (1010,2010), setting the ultra/mega sonic power supply at zero output;after temperature inside bubble cooling down to a set temperature, setting the ultra/mega sonic power supply at frequency f1 and power P1 again;detecting power on time at power P1 and frequency f1 and power off time separately or detecting amplitude of each waveform output by the ultra/mega sonic power supply;comparing the detected power on time with a preset time τ1, or comparing the detected power off time with a preset time τ2, or comparing detected amplitude of each waveform with a preset value, if the detected power on time is longer than the preset time τ1, or the detected power off time is shorter than the preset time τ2, or the detected amplitude of any waveform is larger than the preset value, shut down the ultra/mega sonic power supply and send out an alarm signal.