The Electromagnetic properties of the runways structure are important and meaningful for the quality surveillance, timing maintenance of runways and the correct location of the target underground. The inversion method of the dielectric property and thickness of multilayer media is studied in this paper. Based on the conventional system identification method, the construction of the propagation model and the estimation method of time delay of the echoes are modified in the new method proposed in this paper. The new method considers the relationship of the image part of the permittivity and frequency, and introduces WRELAX method to estimate the time delay of the echoes. The electromagnetic properties and thickness of the runways structure containing the thin layer can be calculated and the estimation precision is improved compared with the conventional system identification method.