Disclosed is a method of final defect inspection, including preparing a final defect inspection apparatus which includes a host device, a microscope, a bar code scanner, a support tool and a signal transceiver, using the host device to calibrate an original point in an outline of the circuit board based on a plurality of original mark positions generated by an electromagnetic pen, using the electromagnetic pen to mark each defect position on the inspection region on the circuit board where any defect is found through the microscope, using the signal transceiver to receive and transmit each defect position to the host device, and using the host device to calculate the coordinate of a scrap region based on a relative position between the original point and each defect position so as to generate a shipment file.