Effects of liquid crystal molecules alignment on the detection of Shack-Hartmann wavefront sensor and closed loop correction are investigated.The effect of molecule alignment on the intensity of parasitic light is analyzed.The effect of parasitic light on detection and correction accuracy was specially discussed among the closed loop correction. With the ratio of parasitic light of 40%, the detection deviation error is 0.4; while the ratio of parasitic light is 8%, the deviation error just have 0.08, and it may be neglected. And the closed loop correction of static distortion was individually done with twisted and parallel alignment LC WFC. To the twisted alignment, PV and RMS were changed from 1.11 μm and 0.25 μm to 1.08 μm and 0.24 μm. It indicates that the parasitic light causes the serious effect on the closed loop correction. For parallel alignment, with the closed loop correction, PV and RMS are reduced from 1.58 μm and 0.22 μm to 0.095 μm and 0.03 μm respectively, and the resolvable image of the fiber bundle is also achieved. The results show that, if the intensity of parasitic light is lower than 8%, high correction accuracy can be obtained.