Conservation tillage (CT) practices, including no-tillage and stover mulching, are increasingly recognized for their capacity to enhance soil health, sequester carbon, and mitigate greenhouse gas emissions in conventional agricultural systems. However, their application and mechanistic implications in medicinal crop cultivation-where soil quality directly influences not only yield but also the accumulation of pharmaceutically active secondary metabolites-remain underexplored. This review synthesizes recent advances in understanding how CT modulates soil microbial communities, with particular emphasis on nosZ II-type denitrifiers, to reduce nitrous oxide (N2O) emissions and improve nitrogen use efficiency. The mechanistic pathways through which CT-induced changes in soil structure, moisture regimes, and organic matter dynamics influence the abundance, community composition, and activity of nitrogen-cycling microorganisms were examined. Based on evidence from black soil ecosystems and other agricultural systems, it is demonstrated that no-tillage with full stover mulching (NT100) selectively enriches specific nosZ II subclades (IIB, IIE, IIG) through deterministic community assembly processes, effectively decoupling N2O emissions from nitrification activity. The implications of these soil improvements for medicinal plant growth, root development, nutrient acquisition, and stress tolerance were further explored, and case studies linking organic amendments, mycorrhizal associations, and microbial inoculants to enhanced accumulation of alkaloids, flavonoids, terpenoids, and saponins were synthesized. Importantly, findings from spatial phylogenetics and biocultural diversity research were integrated to examine how CT can support in situ conservation of medicinal flora and associated microbial communities in ethnomedicinally significant hotspots such as the Hengduan Mountains, southeastern Tibet, and subtropical refugia. Policy and community-based approaches for integrating CT into biocultural conservation strategies are discussed. By bridging agronomy, microbial ecology, phytochemistry, and ethnobotany, a framework for "eco-pharmacological" management is proposed, aligning sustainable soil practices with medicinal crop quality, climate mitigation, and the preservation of both biological and cultural heritage.