The geometric calibration errors of deflectometry are the principle factors that limit the precision of low-order surface measurements. In this study, the relationship between the alignment error of geometric calibration and low-order surface measurement error of a flat mirror is analyzed. Further, the sensitivity equations and weight factors that describe the relationship between the alignment error and surface measurement error are introduced and verified using simulations and experiments. The results denote that the alignment errors will introduce tilt, defocus, astigmatism, and coma aberrations to the surface measurement results. Furthermore, the surface measurement errors are observed to be proportional to the alignment errors. This study aids in achieving a system configuration of deflectometry that can improve the accuracy of the low-order surface measurements and provides a theoretical guide for assessing and analyzing the surface measurement errors associated with the deflectometry measurements.