The principle of chromatographic fingerprint is that certain diagnostic metabolites should be always distributed in a given plant and currently, it has been widely accepted as a promising means for medicinal plant authentication. Moreover, the chemical profile is the only evidence to clarify the ingredients of those consumable plant products, e.g. traditional Chinese medicine (TCM) prescriptions. Herein, efforts were made to describe the diagnostic metabolome of medicinal plant or TCM prescription using a binary code sequence. Forty-five well-known medicinal plants along with six relevant prescriptions were employed for concept illustration and proof. Each plant was subjected to chemical characterization, and diagnostic metabolites of all plants were gathered into a chemical pool containing 595 compounds. A robust method enabling the detection of all 595 constituents was then developed using LC coupled to scheduled multiple reaction monitoring. Analyst™ software was responsible for automatically judging the presence (defined as “1”) or absence (defined as “0”) of each analyte with a defined signal-to-noise threshold (S/N > 100). After converting each medicinal plant to a binary sequence consisting of 595 codes, an in-house database was built by involving all sequences. The potentials of sequence library retrieval towards plant authentication, preliminary chemical characterization, and deformulation of TCM prescriptions were demonstrated after that the diagnostic metabolome of each test sample was translated to a binary code sequence. Above all, binary code is a flexible tool for diagnostic metabolite sequencing of medicinal plants, and it should be an alternative tool of DNA barcoding towards plant authentication.