Beam quality is always an important parameter to value the output quality of laser beam, and many methods are developed. For high intensity laser beam with center obscuration, beam quality far field measurement method is used presently. The beam quality factor β is used to judge the performance parameters of the beam quality in the application of beam transport efficiency field, and it is obtained by CCD far field measurement. In order to advance measurement precision of the CCD far field beam quality factor β measurement system, the key parameters in optical elements and data collecting and processing courses are analyzed, and different calibration methods are used for different parameters. The calibration methods used in practice are explained, and the sources of the system measurement uncertainty are analyzed and determined quantificationally. The research of calibration methods promotes the advance of the measurement method, and the application of the calibration method benefits the improvement of the veracity and reliability of the measurement results in the practical measurement work.