Licorice is a famous Chinese medicinal material widely applied worldwide in food and drugs. It possesses a substantial share in the international and domestic markets. While the demand is continuously increasing, wild-type of licorice is gradually disappearing. Its cultivated-type is significantly different compared to its wild-type, especially the bioactive compounds in dried roots and rhizomes (the medicinal parts of wild and cultivated licorice) are responsible for their quality difference. In this study, a total of thirty-two constituents, including seventeen secondary compounds and fifteen primary metabolites, were simultaneously analyzed by UFLC coupled with triple quadrupole-linear ion trap mass spectrometry (UFLC-QTRAP-MS/MS) in different medicinal parts of licorice. Our findings indicated that the content of major bioactive compounds in wild licorice were significantly higher than those in its cultivated-type. The metabolites in rhizomes showed totally different outcomes between wild and cultivated licorice. Remarkably high level of some important amino acids related to abiotic stress (drought and salt) were found in wild licorice. Notably, the high contents of phenylalanine and compounds in upstream of flavonoid synthesis in cultivated licorice suggested that the synthesis may differ at the initial stage. The distribution pattern of metabolites in different medicinal parts of wild and cultivated licorice will not only provide a novel clue in agricultural breeding but also facilitate the further study on their quality formation.