Background: Herbal and natural medicines play significant roles in treatment of diseases and development of novel drugs. Salsola vermiculata is an annual plant which is broadly distributed in southwest of Asia, and is used for treatment of stomach disorders. Results: This present study aimed at identifying and comparing the metabolic profiles of different parts of Salsola vermiculata and to evaluate the inhibitory potential of their extracts and fractions towards acetylcholinesterase and α-glucosidase. LC-ESI-MS, GC, and GC-MS analytical methods were employed for metabolite profiling of the extracts, and their fractions. The α-glucosidase and acetylcholinesterase inhibitory activities of the samples were determined by microplate colorimetric methods. Based on results, 44 metabolites were identified in different parts of S. vermiculata. In roots, vanillic acid, rutin, salsoline, salsoline A, palmitic acid, oleic acid, linoleic acid, cumin aldehyde, and carvone; in seeds, vanillic acid, salsoline A, palmitic acid, oleic acid, linoleic acid, carvone, and β-caryophyllene; in leaves, gallic acid, vanillic acid, caffeic acid, rosmaric acid, rutin, quercetin, limonene, and carvone, and in flowers, gallic acid, vanillic acid, cinnamic acid, rosmaric acid, rutin, kaempferol, limonene, linalool, and carvone were recorded as the main components. According to the inhibitory activities results, the ethyl acetate fractions of leaves and the aqueous-acid fraction of roots displayed highest inhibitory activity towards acetylcholinesterase (IC50: 17.24 µg/mL), and α-glucosidase (IC50: 62.37 µg/mL), respectively. Conclusion: Finally, the leaves and roots of S. vermiculata are rich of phenolic and alkaloids compounds and the findings of this study depict them as a promising acetylcholinesterase and α-glucosidase inhibitors, and therefore, can be utilized for the development of new drugs.