This study was conducted to investigate the chemical differences between Acori Tatarinowii Rhizoma and Acori Calami Rhizoma using gas chromatography with mass spectrometry and chemometric methods. Quantitative fingerprints were established. A total of 90 volatile compounds were identified and quantified using heuristic evolving latent projection and retention index. An efficient model based on partial least squares-discriminant analysis coupled with variable iterative space shrinkage approach was developed to distinguish Acori Tatarinowii Rhizoma from Acori Calami Rhizoma. The correct rate was 95.83%, and the area under the receiver operating characteristic curve was 100%. Finally, three volatiles, namely, camphor, longicyclene, and δ-cadinene, were selected as key discrimination factors between Acori Tatarinowii Rhizoma and Acori Calami Rhizoma. The proposed protocol can serve as a valid strategy for quality control and screening of potential bioactive components of herbal medicines.