The present invention provides a method and a system for measurement of thickness of non-metallic materials by employing Terahertz waves. The method comprises the steps of: Terahertz waves are vertically incident into the surface of non-metallic materials, the Terahertz waves are reflected by the surface and the bottom surface of the non-metallic materials to respectively form first reflection signals and second reflection signals, the first and second reflection signals are received, and a receiving time difference [Delta]T1 of the two reflection signals is obtained; the Terahertz waves are incident into the surface of the non-metallic materials at an angle of [Theta]i, the Terahertz waves are reflected by the surface and the bottom surface of the non-metallic materials to respectively form third reflection signals and fourth reflection signals, the third reflection signals and the fourth reflection signals are received, and a receiving time difference [Delta]T2 of the two reflectionsignals is obtained, wherein [Theta]i is larger than 0 degree and smaller than 90 degrees; a refractive index n of the non-metallic materials is obtained according to the receiving time difference [Delta]T1 and the receiving time difference [Delta]T2; and the thickness d of the non-metallic materials is obtained according to the refractive index n of the non-metallic materials. The method can directly measure the refractive index and the thickness of the non-metallic materials, and is small in measurement error and high in accuracy.