Fused Deposition Modeling(FDM) is a most widely applied material forming technology for 3D printer. Nevertheless, there is no standardized method for error analysis of 3D printing based on FDM. Polymer materials commonly used in FDM has a strong absorption in terahertz range. Using the method of injecting water into the apertures of specimens, error analysis of both the physical area and non-physical area of specimens is successfully realized by Terahertz Time Domain Spectroscopy(THz-TDS). Based on the analysis of terahertz spectrum, the micron error of 0.96% is able to be observed.