Geo-authentic herbs refer to medicinal materials produced in a specific region with superior quality. Stephania tetrandra S. Moore (S. tetrandra) is cultivated in many provinces of China, including Anhui, Zhejiang, Fujian, Jiangxi, Hunan, Guangxi, Guangdong, Hainan, and Taiwan, among which Jiangxi is the geo-authentic origin. To explore habitat-related chemical markers of herbal medicine, an integrated chromatographic technique including gas chromatography-mass spectrometry (GC-MS), ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS) and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) combined with chemometric analysis was established. The established methods manifested that they were clearly divided into two groups according to non-authentic origins and geo-authentic origins, suggesting that the metabolites were closely related to their producing areas. A total of 70 volatile compounds and 50 non-volatile compounds were identified in S. tetrandra. Meanwhile, tetrandrine, fangchinoline, isocorydine, magnocurarine, magnoflorine, boldine, and higenamine as chemical markers were accurately quantified and suggested importance in grouping non-authentic origins and geo-authentic origins samples. The discriminatory analysis also indicated well prediction performance with an accuracy of 80%. The results showed that the multiple chromatographic and chemometric analysis technique could be used as an effective approach for discovering the chemical markers of herbal medicine to fulfill the evaluation of overall chemical consistency among samples from different producing areas.