Chinese hawthorn (Crataegus pinnatifida) offers both medicinal and nutritional benefits due to its bioactive compounds. However, the combined effects of environmental and anthropogenic factors on its geographic distribution and medicinal quality remain insufficiently explored. Species distribution modeling (Biomod2) was integrated with ArcGIS-based spatial analysis to systematically model suitable habitats for C. pinnatifida across varying environmental and anthropogenic conditions, while concurrently assessing the spatial distribution patterns of medicinally active compounds. Furthermore, multi-scenario climate simulations were utilized to predict the impacts of future climate change on the spatial distribution patterns of this species. Anthropogenic activities strongly influence C. pinnatifida habitat suitability, followed by BIO18 (Precipitation of Warmest Quarter) and BIO4 (Temperature Seasonality). Bioactive compound heterogeneity is driven by anthropogenic activities, AWC (Soil Available Water Content), BIO12 (Annual Precipitation), and BIO4. High-suitability/high-quality areas are concentrated in Shandong Province. Under SSP126 (low emissions), high-suitability areas remain stable (2050s–2090s) with northeastward centroid shifts; under SSP585 (high emissions), they contract with southeastward centroid migration. Shandong is the optimal long-term cultivation region across scenarios. These findings establish a critical basis for cultivating C. pinnatifida with enhanced medicinal properties, developing adaptive management strategies to strengthen conservation, and ensuring sustainable utilization amid global climate change.

Background: Cultivation environments impose distinct abiotic and biotic stresses that act as primary drivers reshaping the metabolic profile and microbiome assembly of medicinal plants. This study investigates the impact of simulative habitat versus arched greenhouse cultivation on the synthesis of bioactive ginsenosides and the associated root microbiome structure in Panax ginseng. Methods: A combined metabolomics and microbiomics approach was applied to compare ginsenoside accumulation and rhizosphere microbial community composition under the two cultivation modes. Results: Ginseng from simulative habitat cultivation exhibited significantly higher ginsenoside content, particularly ginsenoside Re, compared to arched greenhouse cultivation, with this advantage being more pronounced in long-term cultivation. Microbiome profiling revealed that specific taxa, including Bradyrhizobium, were strongly enriched in simulative habitats and positively correlated with enhanced ginsenoside accumulation, suggesting a microbiome-mediated mechanism for metabolic plasticity. In contrast, arched greenhouse cultivation was associated with a more complex microbial structure characterized by increased negative interactions, which may compromise metabolic quality. Conclusions: These findings, utilizing multi-omics correlations, provide a theoretical basis for optimizing Panax ginseng quality through ecological cultivation strategies that leverage stress-responsive microbe–metabolite interactions.