To verify the thermal blooming effect while high energy laser propagates through the atmosphere above the water surface, an innovative method of scaled experiment was applied to overcome the difficult of complexity and expensiveness of high energy laser system with big aperture. One effective experimental method of laser propagation through water surface was designed based on theoretical analysis. The wavelength of laser is about 1000nm. The experimental results show that: The thermal blooming could be ignored while choosing suitable laser power and beam diameter. And the results are also helpful for the design of high energy laser system with big aperture.