Weiwei Zhao’s research exemplifies excellence in soil science through her innovative investigations into rhizosphere ecology and plant–soil interactions, particularly focusing on the endangered Paeonia ludlowii in the Tibetan Plateau. Her studies explore how diverse soil physicochemical properties, enzyme activities, and microbial communities influence the metabolic pathways of medicinal plants across different habitats. Employing advanced tools such as high-throughput sequencing and GC-TOFMS metabolomic profiling, her work provides valuable insights into soil metabolites and their regulatory networks, linking soil health to plant bioactive compounds. Her comparative analyses of chloroplast genomes and genetic diversity using ISSR markers contribute significantly to understanding germplasm conservation, hybrid breeding, and adaptive evolution of peony species. Through extensive field investigations, data analysis, and collaboration with regional agricultural and horticultural institutes, she advances sustainable approaches for plateau ecosystem management, ornamental plant domestication, and genetic improvement. Her multidisciplinary contributions bridge soil chemistry, plant physiology, and molecular biology, establishing a scientific foundation for conserving endangered flora and enhancing medicinal resource utilization. Her impactful publications in indexed journals further highlight her commitment to advancing soil metabolomics, microbial ecology, and biodiversity conservation within complex high-altitude environments, reinforcing her status as a leading innovator in soil–plant interaction research.