Computational vibrational spectroscopy serves as an important tool in the interpretation of experimental infrared (IR) spectra. In this article, we present a systematic benchmarking study of DFTB3 with two different computational vibrational spectroscopic methods, based on either normal mode analysis (NMA) or fast Fourier transform dipole autocorrelation function (FT‐DAC). The results were compared with experimental data and theoretical calculations with B3LYP/cc‐pVTZ. The empirical scaling factors for DFTB3/NMA, DFTB3‐freq/NMA, and DFTB3/FT‐DAC methods are 0.9993, 1.0059, and 0.9982, respectively. We also demonstrate the significance of anharmonicity and conformational sampling in vibrational spectroscopic calculations on flexible molecules. As expected, DFTB3/FT‐DAC predicted the anharmonic vibrational peaks more accurately than DFTB3/NMA and NMA spectra are highly dependent on the initial structures. The potential limitations of DFTB3 for vibrational spectroscopic calculations and the challenges in assigning the FT‐DAC spectral peaks were noted. DFTB3/FT‐DAC is expected to serve as a promising technique in computational spectroscopy in complex biomolecular systems.