SummaryCrop domestication usually leads to the narrowing genetic diversity. However, human selection mainly focuses on visible traits, such as yield and plant morphology, with most metabolic changes being invisible to the naked eye. Buckwheat accumulates abundant bioactive substances, making it a dual‐purpose crop with excellent nutritional and medical value. Therefore, examining the wiring of these invisible metabolites during domestication is of major importance. The comprehensive profiling of 200 Tartary buckwheat accessions exhibits 540 metabolites modified as a consequence of human selection. Metabolic genome‐wide association study illustrates 384 mGWAS signals for 336 metabolites are under selection. Further analysis showed that an R2R3‐MYB transcription factor FtMYB43 positively regulates the synthesis of procyanidin. Glycoside hydrolase gene FtSAGH1 is characterized as responsible for the release of active salicylic acid, the precursor of aspirin and indispensably in plant defence. UDP‐glucosyltransferase gene FtUGT74L2 is characterized as involved in the glycosylation of emodin, a major medicinal component specific in Polygonaceae. The lower expression of FtSAGH1 and FtUGT74L2 were associated with the reduction of salicylic acid and soluble EmG owing to domestication. This first large‐scale metabolome profiling in Tartary buckwheat will facilitate genetic improvement of medicinal properties and disease resistance in Tartary buckwheat.