The invention discloses a substrate glass defect treatment system. The substrate glass defect treatment system comprises a substrate glass conveying device (100), a defect recognition device (200), a defect removing device (300), a defect collecting device (400) and a controller, wherein substrate glass (10) is arranged on the substrate glass conveying device and conveyed in the length direction of the substrate glass conveying device; the defect recognition device is arranged on one side of the substrate glass conveying device in the width direction of the substrate glass conveying device, and is arranged by facing the substrate glass; the defect recognition device is used for recognizing and positioning coordinate positions of defects; the defect removing device is arranged at the downstream of the defect recognition device in the conveying direction of the substrate glass conveying device; the defect removing device is used for separating glass defects from the substrate glass; the defect collecting device is arranged on the opposite side of the defect removing device, and is used for receiving the separated glass defects; the controller is electrically connected with the substrate glass conveying device (100), the defect recognition device (200), the defect removing device (300) and the defect collecting device (400) respectively and is used for controlling coordinated operation thereof.