Metabolites of Heihe 43 soybeans in three origins (Beian Longmen, Weishan and Yinlong River) were isolated and identified using non-targeted metabolic profiling based on gas chromatography-mass spectrometry. The metabolites in the soybean samples were extracted by 80% methanol, derivatized with N,O-bis (trimethylsilyl) trifluoroacetamide, eluted on an HP-5ms column, detected with GC-MS. The metabolic pathways of the differential metabolites were analyzed by KEGG annotation, the metabolic mechanisms were explored. A total of 68 metabolites were detected in soybean samples, and 62 metabolites were isolated and identified, included 22 carbohydrates and their derivatives, 14 fatty acids and their derivatives, 7 alcohols, 4 esters, and 2 amino acids, and 13 kinds of intermediates, inferring the structure of 6 kinds of unknown metabolites, 4 kinds of WS-soy samples, 2 kinds of YLH-soy samples. Soybean metabolites and metabolic mechanisms were different in different producing areas, and they had the attributes of producing areas. This not only provides a theoretical basis for the quality analysis of soybeans in cold regions, and also provides a basis for soybean classification and processing or extraction of functional components by origin.