The detection and alignment of polarization axis is a key technology in PMF’s application.In order to improve the accuracy of the end face detection of polarization axis,a sub-pixel edge extraction method based on surface fitting was proposed to improve the accuracy and the normal distribution of the detection result was used to improve the precision.Based on the normal distribution of the detection result,a aligning method based on normal distribution was put forward.An automatic aligning system was established.The experiment shows the sub-pixel edge extraction method can decrease the error by 45% and the ellipse fitting can reduce the error by 15%.The alignment experiment figures out that the bias of aligning method based on probability is less than 0.1°.