The present invention relates to a debugging apparatus for a computer system and a method thereof. A detecting unit detects if a debugging unit connects to the computer system. When a debugging unit connects to the computer system, the detecting unit produces a detecting signal, which contains information of a bus in the computer system electrically connected with the debugging unit. Then a selection unit selects the bus electrically connected with the debugging unit according to the detecting signal. Besides, a testing unit tests the computer system and produces a power-on self-test (POST) code, so that the selected bus can be used for outputting the POST code to the debugging unit. Thereby, the present invention can choose to use the bus reserved in the computer system for outputting the POST code to the debugging unit, and hence facilitating inspection personnel to debug the computer system.