Medicinal food homologous (MFH) substances not only provide nutrition but also serve as a traditional means to overcome many health issues. Authentication of these products verifies their efficacity and assures consumers of a genuine product. In this review paper, we focus the determination of MFH authenticity including geographical identification and adulteration detection using mass spectrometry (liquid and gas chromatography) based metabolites and inorganic constituents (muti-elements and stable isotopes). The application of these techniques to determine product identification characteristics combined with chemometrics are discussed, along with the limitations of these techniques. Multi-elements, stable isotopes, and metabolite analysis are shown to provide an effective combination of techniques to resolve the origin of various MFH products. Most organic compounds from MFH products are identified using chromatographic separation techniques (HPLC, GC) combined with different detection methods. Chemometric analysis of organic and inorganic fingerprints offers a robust method to detect and classify mislabeled and suspected fraudulent samples of different MFH products.