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Climate change profoundly influences the geospatial distribution of secondary metabolites and causes the geographical migration of plants. We planted seedlings of the same species in eighteen ecological regions along a latitudinal gradient in eastern and western China, in order to explore the regulation of multi-climatic factors on active ingredient accumulation in Salvia miltiorrhiza Bunge. The correlations between six active ingredient contents and ten climatic factors were investigated to clarify their relationships. We found that climatic factors not only regulated active ingredient contents but also markedly influenced their composition and led to a specific geospatial distribution of these active ingredients in China. The main climatic factors include the air temperature, precipitation, atmospheric vapour pressure and sunshine duration. Future warming in high-latitude regions could cause continued northward expansion of planting areas suitable for S. miltiorrhiza. The effect of extreme climatic conditions on active ingredients should not be overlooked. The findings of this study can help farmers scientifically choose suitable cultivation regions in the future. Furthermore, this study provides an innovative idea for the exploration of secondary metabolic responses to changing ecological factors in medicinal plants.