To explore the effect of ecological factors on the features of ginsenosides and amino acids of mountainous forest cultivated ginseng (MFCG) and distinguish it from garden ginseng (GG). The main active constituents of ginsenosides and primary metabolites-amino acids of MFCG were determined by the high-performance liquid chromatography with diode array detector (HPLC-DAD) technique; The climatic factors were obtained by Geographic Information System for Global Medicinal Plants (GMPGIS), and the topographic factors were recorded at the place of origin; Mineral elements in rhizosphere soils of MFCG were determined by inductively coupled plasma mass spectrometry (ICP-MS), inductively coupled plasma optical emission spectrometry (ICP-OES) and atomic absorption spectrometry and other rhizosphere soil factors, inclusive of pH and available N, P and K. The findings indicated that the warmer, relatively humid, and relatively shady environments are suitable for the accumulation of ginsenosides of MFCG, in addition, they were also influenced by its rhizosphere soil. Contrastingly, conditions of lower temperature, more precipitation, weaker light, and higher altitude are beneficial to the accumulation of amino acids; Additionally, mineral elements are conducive to the accumulation of amino acids, while soil acidification is unfavorable. Surprisingly, the present study found that the temperature could regulate ginsenosides and amino acids in an opposite direction, and the ecological environment has a greater effect on primary metabolites of amino acids than secondary metabolites of ginsenosides. Finally, the Ser, Arg, Gly, Thr, Pro, Cys, Ile, Leu, Phe, Tyr, and GABA in MFCG were lower than those in GG (p < 0.01); The dencichine (p < 0.05) and dencichine/GABA (p < 0.01) in MFCG were higher than those in GG. Among them, the average ratio of dencichine to GABA is about 6:1 in MFCG and 3:1 in GG in most instances. It is for the first time that the effects of ecological factors on the chemical composition of MFCG and its distinction from GG by amino acids were investigated. Display omitted •Ecological environment has a greater effect on primary metabolites than secondary metabolites.•Temperature can regulate ginsenosides and amino acids in an opposite direction.•Minor amounts of heavy metal elements are useful for the accumulation of food composition.•Key ecological factors of mountainous forest cultivated ginseng were identified.•The characteristics of amino acids in mountain- and garden- cultivated ginseng.