Measurement errors in frequency domain always appear when testing samples’ terahertz (THz) absorption spectrum using terahertz time-domain spectroscopy (THz-TDS) system, which is supposed to be attributed to the sampling accuracy of the high speed electro-optic sampling system. In order to make the measurement have a high accuracy, the method of error correction was studied in the present article. Carbon monoxide in gas phase was employed as our standard sample, and its absorption spectrum at the pressure of 2.0×105 Pa was measured experimentally. Comparing the obtained absorption frequencies with the corresponding standard data in JPL database, we got the error values, and their distribution law shows that the values have a linear correlation with the standard absorption frequency. Based on this, the error correction model was built. Using the model to correct the experimental data, the result shows the maximum error after correction is reduced to 3.36 GHz, which is two orders of magnitude lower than the error before correction. This states that the model can be used to correct the error of the THz spectrum caused by high speed electro-optic sampling system. At last, the authors draw a conclusion that the THz-TDS system is supposed to be corrected by the terahertz spectrum of carbon monoxide before measurement, in this way, the terahertz spectrum of sample can have a high accuracy. The study contributes to the material identification and the construction of molecular spectroscopy database in THz region.