Abstract: The quality of Panax notoginseng medicinal herbs affects their clinical treatment efficacy. At present, the quality of Panax notoginseng varies greatly, and its quality control mainly relies on saponin compounds, which cannot systematically reflect the quality of Panax notoginseng medicinal materials. This study is based on the collection of Panax notoginseng medicinal materials from different production areas, using micromethod, UV visible spectrophotometry, and high-performance liquid chromatography to quantitatively analyze multidimensional indicators that affect the efficacy and formulation of Panax notoginseng. The results showed that the production area with high content of macromolecules (amylum, cellulose, lignin) in Panax notoginseng was Yanfangxiang, Zhanyi, Qujing, Yunnan. The production area with high content of total polysaccharides was Malipo, Malizhen, Wenshan, Yunnan. The production area with high content of total flavonoids was Qinglongzhen, Huaning, Yuxi, Yunnan. And the production area with high content of Panax notoginseng was Dianshaxiang, Xundian, Kunming, Yunnan. The production area with high content of total saponins was Malipo, Malizhen, Wenshan, Yunnan. Based on hierarchical clustering and orthogonal partial least squares-discrimination analysis (OPLS-DA), dencichine, total polysaccharides, amylopectin, and cellulose were identified as potential biomarkers for distinguishing Panax notoginseng medicinal materials from different production areas. Using the global geographic information system for medicinal plants, 19 ecological factors of Panax notoginseng production areas were obtained, and the impact of ecological factors on the accumulation of various components of Panax notoginseng was determined through correlation analysis. Among them, the annual precipitation, the isothermality, the mean diurnal range, the min temperature of coldest month, the mean temperature of warmest quarter, the precipitation of wettest quarter, and the precipitation of warmest quarter were key ecological factors affecting the quality of Panax notoginseng. In summary, this study comprehensively evaluated the quality of Panax notoginseng from different origins, revealed the key ecological factors that affect its authentic quality, and provided a reference for subsequent quality control and rational site selection of Panax notoginseng.