It is made clear that the sources of the amplitude uncertainty for Terahertz Time-Domain Spectroscopy(THz-TDS) system are registration jitter and sampling jitter of delay line and the femtosecond laser power fluctuation. The method of combination of theory and experiment is utilized to prove that registration jitter and sampling jitter of delay line affect the accuracy of the refractive index extracted by THz-TDS system, while sampling jitter of delay line and laser power fluctuation affect the accuracy of the high and low frequency parts of absorption coefficient extracted by THz-TDS system respectively.