In high-power laser system, mid-spatial-frequency wavefront of large flat influences safety of the system and root mean square of mid-spatial-frequency wavefront (PSD1) is used to evaluate corresponding wavefront. Because large-aperture interferometer can′t fully meet the demand of the need of system transfer function (STF) for testing mid-spatial-frequency wavefront, a statistical method based on small-aperture interferometer is proposed, and the uncertainty is analyzed. Testing system is set up, and the sub-region tilt compensating method is developed. Testing resolution is improved. Theoretical and experimental result shows that for 400 mm×400 mm analyzing region, when the number of sub-region is set to 4×4 and confidence level is 95.4%, uncertainty is ±0.266 nm. In comparing test with large-aperture interferometer, deviation between two methods in analyzing region of 400 mm×400 mm is less than 5%. Sub-region statistical analyzing method is a useful compensation for large-aperture testing method and plays a critical role for optimization of advanced optical fabrication technics.