The invention belongs to the field of product identification, and provides a two-dimension code scanning system and a scanning and calibration method and system thereof. According to the method and system, a spell, instantaneously starting after the current counting carried out by a two-dimension code scanner and a photoelectric sensor in the two-dimension code scanning system is finished, is selected to serve as an adjustable time difference parameter, and therefore a computer can complete calibration between the end of the current counting carried out by the two-dimension code scanner and the photoelectric sensor and the end of next initial counting by adjusting the time difference parameter. By means of the method and system, when on-site environmental factors change, specification of motion rules when two-dimension codes are continuously scanned is carried out, the time difference parameter can be smaller than the time between the current counting carried out by the two-dimension code scanner and the photoelectric sensor and the end of next initial counting, real-time scanning and calibration are automatically triggered, calibration precision, namely the error range, desired calibration precision, namely, the error range is achieved, therefore accurate real-time automatic calibration is achieved, and applicability of the two-dimension code scanning system is improved.