In order to ensure the accuracy evaluation of 3D surface topography, and eliminate the effect of impulse noise and basic deflection surface generated in measuring process, an evaluation method of 3D surface topography was proposed based on the improved median filter and least square method. The impulse noise of 3D surface topography was removed by the improved median filter, and the basic deflection surface was generated by the least square method. The evaluation surface was generated by removing the impulse noise and basic deflection surface, and the roughness surface was extracted by the Gaussian filter method and the typical evaluation parameters were calculated. The experimental result shows that the typical evaluation parameters of the evaluation surface can more exactly reflect 3D surface topography.