We present a specific-window method to subtract the interference of water vapor on terahertz frequency-domain spectroscopy (THz-FDS) at ambient temperature and pressure. A continuous-wave spectrometer based on photomixing was utilized to obtain THz-FDS of methanol vapor in the range of 50–1200 GHz. The distinctly spaced absorption features in the neighborhood of atmospheric windows of transparency were selected to perform linear fitting versus the calculated absorption cross section and obtain the concentration of methanol. Furthermore, the gradually decreased methanol vapor was quantified to demonstrate the reliability of the method.