Disclosed is a final defect inspection system, which including a host device, a microscope, a bar code scanner, a support tool, a signal transceiver and an electromagnetic pen. The bar code scanner scans a bar code on a circuit board provided on the support plate. The host device selects data and a circuit layout diagram from the database corresponding to the bar code. The signal transceiver and the electromagnetic pen are electrically connected to the host device. The electromagnetic pen is used to make a mark on a scrap region of the circuit board where any defect is visually found through the microscope. The signal transceiver receives and transmits the positions of the mark to the host device such that the host device calculates the coordinate of a scrap region based on a relative position between an original point and the positions of the mark.