The analysis on the thickness of polyamide plate using Terahertz Time Domain System (THz-TDS) in reflection mode is carried out. The refractive index, one of the optical parameters in terahertz band, is solved through the mathematics model, and its value is 1.88. A kind of polyamide plate sample with four kinds of thickness is designed and the ability of THz-based method to detect defects or foreign bodies in fiber glass is verified by attaching metal plates to the back of fiberglass. By the comparison of traditional method and THz method, the terahertz method has a measurement error between 2.5% and 10%. As the thickness increases, the error tends to increase. The reason about the deviations is analyzed, as well as the systematic factors affecting the thickness measurement accuracy, in order to improve the accuracy of THz thickness measurement system and provide theoretical basis for designing terahertz thickness measurement system in the future.