Soil desertification and sustainable cash crop cultivation in arid regions are pressing global challenges. This study aims to investigate two ecotypes of the drought-tolerant medicinal plant Cistanche sinensis, sourced from loamy (HCS) and sandy (GCS) soil habitats, to elucidate their rhizosphere and endophytic microbial communities and metabolic profiles, uncovering the mechanisms underlying their ecological adaptation and quality variation. Using multi-omics, machine learning, antioxidant assays, and soil analyses, we characterized the microbial communities and metabolomes of both ecotypes. The GCS ecotype showed potential for environmental remediation and medicinal applications, while the HCS ecotype enhanced soil quality and yielded consumable products. A regulatory network analysis identified key microbial genera (Mycobacterium, Phyllobacterium, Pseudogymnoascus, Fusarium) that differentiate the ecotypes. Phenylpropanoid compounds, crucial for medicinal properties, were more abundant in GCS. Machine learning identified 13 bioactive compounds, with 10 associated with GCS and 3 with HCS. HCS exhibited superior antioxidant capacity. The influence of microbial communities was ranked as follows: rhizosphere bacteria > rhizosphere fungi > endophytic fungi > endophytic bacteria, with bacteria promoting and fungi inhibiting medicinal metabolism. The GCS ecotype is a promising candidate for biofertilizer development, leveraging Mycobacterium, Anseongella ginsenosidimutans, and Fusarium equiseti, while also requiring strategies to mitigate root-associated pests and diseases. For the HCS ecotype, Mortierella alpina emerged as a potential biofertilizer candidate. These findings offer insights into desertification adaptation, a framework for studying ecotype quality variations, and strategies to enhance the ecological and nutraceutical value of C. sinensis through microbial and fertilizer management.