With the objective of collecting more accurate results and improving the testing accuracy during the mirror substrate manufacturing and generating phase, the adjustment theory to measure the large aperture mirror profile based on the instrument of laser tracker was adopted. Firstly, the adjustment theory was deduced and the main influence factors for the accuracy of the profile metrology was obtained, then the fitting model of profile of the large aperture mirror was established. And then a method to improve the metrology accuracy for the fitting model was proposed. Lastly, the method was applied to the two meter class in diameter substrate of SiC primary mirror, and the theory was verified from the different aspects of F number, residual error and structure function. The proposed method could be showed as a guideline to the metrology and manufacture of large aperture mirror.