Terahertz time-domain spectroscopy (THz-TDS) systems are widely used to obtain fingerprint spectra of many different biomedical substances, and thus the identification of different biological materials, medicines, or dangerous chemicals can be realized. However, the spectral data for the same substance obtained from different THz-TDS systems may have distinct differences because of differences in system errors and data processing methods, which leads to misclassification and errors in identification. To realize the exact and fast identification of substances, spectral standardization is the key issue. In this paper, we present detailed disposal methods and execution processes for the spectral standardization and substance identification, including feature extracting, database searching, and fingerprint spectrum matching of unknown substances. Here, we take twelve biomedical compounds including different biological materials, medicines, or dangerous chemicals as examples. These compounds were analyzed by two different THz-TDS systems, one of which is a commercial product and the other is our verification platform. The original spectra from two systems showed obvious differences in their curve shapes and amplitudes. After wavelet transform, cubic spline interpolation, and support vector machine (SVM) classification with an appropriate kernel function, the spectra from two systems can be standardized, and the recognition rate of qualitative identification can be up to 99.17%.