Using THz-TDS to detect the THz temporal pulse and calculate the absorption spectrum of the sample is the main access to qualitative and quantitative analysis. The shape and the amplitude of the THz absorption spectra are not only related to the sample, but also closely related to the length of the chosen THz pulse in the calculation, which was discovered in our experiments. It is the main cause of this problem that the flaky sample reflects the THz wave many times, which will give rise to the Fabry-Perot effect. So the sample-probing temporal signal is divided into the intrinsic section with the sample’s information directly, low SNR noise section, and unwanted Fabry-Perot reflections section with the overlapped information. Based on THz pulse generation mechanism and the relationship between the pulse amplitude and the attenuate process, a model of intercepting the intrinsic section in terahertz time-domain pulse was proposed and was proved reliable and stable by the results from experiments performed with amino acids: glutamine(Gln), histidine(His), and cystine(Cys).