This paper analyzes the principle of wavefront disturbed by the free vortex aerodynamic window(FADW) designed for the high power laser measurement using the Hartmann Shack (H S) sensing, and measures the wavefront when the FADW is running steadily using the H S sensor with 37 sub apertures experimentally. The wavefront attained by CCD detectors is sent to the high speed DSP wavefront processing units. And then it reconstructs the disturbed wavefront using the method of Zernike mode, and calculates the relative optical parameters such as the peak value (PV) of wavefront error, RMS and STREHL raton (R s) and so on.The results shows that the effects on the output laser wavefront of the FADW are mainly the beam deflexion and the beam divergence, otherwise the else high level wavefront errors are very low.