| Summary: | (1) Background: The structure, function, and community interactions of soil microbial communities of cultivated <i>Meconopsis integrifolia</i> were characterized by studying this alpine flower and traditional endangered Tibetan medicine. (2) Methods: Soil bacteria and fungi were studied based on high-throughput sequencing technology. Bacteria were isolated using culturomics and functionally identified as IAA-producing, organic phosphorus-dissolving, inorganic phosphorus-dissolving, and iron-producing carriers. (3) Results: The dominant bacterial phyla were found to be Proteobacteria and Acidobacteria, and <i>unclassified_Rhizobiales</i> was the most abundant genus. Ascomycota and Mortierellomycota were the dominant fungal phyla. The bacteria were mainly carbon and nitrogen metabolizers, and the fungi were predominantly Saprotroph—Symbiotroph. The identified network was completely dominated by positive correlations, but the fungi were more complex than the bacteria, and the bacterial keystones were <i>unclassified_Caulobacteraceae</i> and <i>Pedobacter</i>. Most of the keystones of fungi belonged to the phyla Ascomycetes and Basidiomycota. The highest number of different species of culturable bacteria belonged to the genus <i>Streptomyces</i>, with three strains producing IAA, 12 strains solubilizing organic phosphorus, one strain solubilizing inorganic phosphorus, and nine strains producing iron carriers. (4) Conclusions: At the cost of reduced ecological stability, microbial communities increase cooperation toward promoting overall metabolic efficiency and enabling their survival in the extreme environment of the Tibetan Plateau. These pioneering results have value for the protection of endangered <i>Meconopsis integrifolia</i> under global warming and the sustainable utilization of its medicinal value.
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