A computer system and a debugging method thereof are provided. The computer system includes a circuit board, a memory, a circuit board image, and a processor. The circuit board includes a plurality of connection interfaces configured to be electrically coupled to a plurality of hardware devices. The memory stores a basic input/output system program. The basic input/output system program includes a power-on self-test program. The processor loads the basic input/output system program to perform a boot process when the computer system is powered on, reads and executes the power-on self-test program to detect the hardware devices electrically coupled to the connection interfaces, displays the circuit board image on a display, and displays a mark pattern on the circuit board image corresponding to a position of a connection interface image of an abnormal hardware device when the hardware device is detected to be abnormal.