Understanding how medicinal plants adapt to environmental changes is critical for optimizing their growth, yield, and pharmacological quality. This study investigates the adaptive mechanisms of Schisandra sphenanthera following ecological migration from Luanchuan (LC) to Tongdao (TD), focusing on the interplay between metabolic reprogramming, microbial community dynamics, and transcriptional regulation. Utilizing an integrative multi-omics approach—combining metabolomics (HPLC-MS), transcriptomics (RNA-seq), and metagenomics—we identified 2,627 metabolites, 57,061 unigenes, and significant shifts in microbial community structures. Notably, the accumulation of lignans (e.g., Schisandrin A, B, C) and triterpenoids (e.g., hydroxymexicanoic acid, ganoderic acid) significantly increased in TD, while flavonoid compounds (e.g., apigenin, daidzein) decreased, indicating a resource allocation trade-off consistent with the ”energy allocation hypothesis.” Concurrently, rhizosphere microbial communities shifted from Alphaproteobacteria dominance in LC to Actinobacteria prevalence in TD, with implications for nitrogen fixation and pathogen suppression. Transcriptomic analyses revealed extensive reprogramming, with upregulation of key genes ( PAL, 4CL, SQS) linked to secondary metabolism, and Weighted Gene Co-expression Network Analysis (WGCNA) highlighted MAPK signaling pathways mediating plant-microbe interactions. These findings elucidate a complex regulatory network where environmental stress triggers microbial community restructuring, transcriptional reprogramming, and secondary metabolism remodeling, ultimately facilitating ecological adaptation.