The invention belongs to the technical field of calibrating of an apparatus, and discloses a method and a system for calibrating a laser beam analyzer. The structured parallel light field forms a flat top beam with a standard beam width through a diaphragm with a standard aperture; and the calibrated laser beam analyzer measures the beam width of the flat top beam, and compares the measured value with the light beam width standard value to achieve calibrating of the laser beam analyzer. The method and the system are effective and feasible, accurate and stable, and simple and convenient to operate; and the traceability issues of the measured beam width value of the laser beam analyzer are solved, and the calibrating accuracy is greatly improved.