A measuring method for the alignment of polarization axis in direct coupling of Y waveguide modulator to the polarization maintaining fiber（PMF）coil is presented. For precisely measuring the polarization axis, an online measurement system including an optical path and an image processing unit is designed and accomplished. End-view image of the two paralleled component-Y waveguide and fiber component will be imaged to CCD target surface by inserting the detected path into the direct-coupled process. The process system is used to judge the parallel relationship between the two end edges in the captured image and acquire angle deviation of polarization axis. The waveguide -PMF alignment experimental result shows that the measured data fit the calculated line well. And the measurement error is less than 1°, which means that the polarization crosstalk of the coil pigtail is better than -35 dB caused by the angular error of polarization axis. It is confirmed that the accuracy of the end-view measurement method is feasible for alignment of polarization axis indirect coupling of Y waveguide modulator to the PMF coil.