THz time domain spectroscopy often faces a trouble of sample thickness measurement. The thickness measurement often has drawback of physical pressure to affect the real thickness and induce the thickness uncertainty especially for the soft or un-flat sample. In this paper, we compare transmission and reflection of THz waveforms with reference. From very simple calculations, the sample thickness of measured region is determined by the time difference of peak between reference and transmitted THz radiation waveform. Measurement limitation induced thickness uncertainty of system is also discussed. This method is also suitable for on-line large area thickness and uniformity monitor for semiconductors with unknown or not uniform refractive index.