As an effective method, the fingerprint technique, which emphasized the whole compositions of samples, has already been used in various fields, especially in identifying and assessing the quality of herbal medicines. High-performance liquid chromatography (HPLC) and near-infrared (NIR), with their unique characteristics of reliability, versatility, precision, and simple measurement, played an important role among all the fingerprint techniques. In this paper, a supervised pattern recognition method based on PLSDA algorithm by HPLC and NIR has been established to identify the information of Hibiscus mutabilis L. and Berberidis radix, two common kinds of herbal medicines. By comparing component analysis (PCA), linear discriminant analysis (LDA), and particularly partial least squares discriminant analysis (PLSDA) with different fingerprint preprocessing of NIR spectra variables, PLSDA model showed perfect functions on the analysis of samples as well as chromatograms. Most important, this pattern recognition method by HPLC and NIR can be used to identify different collection parts, collection time, and different origins or various species belonging to the same genera of herbal medicines which proved to be a promising approach for the identification of complex information of herbal medicines.