Abstract: Over 40% of the arable lands in the world are acidic soils, where low nutrient availability is the major limiting factor for crop production. Root is not only the main organ for nutrient and water acquisition but also the primary interface for communication interactions between plants and soil microorganisms. Exploring the genetic potentials in roots for nutrient acquisition and utilization, as well as improving the composition and activity of microbes in the rhizosphere, have become the important strategies for increasing crop yield while reducing environmental pollution and promoting soil health. Moreover, nitrogen (N) fixed by legumes in symbiosis with rhizobia provides an irreplaceable clean N source in agro-ecosystems, and the symbiosis is also an important factor influencing rhizo-microbiome. Here, we took soybean as an example to summarize the progress of genetic improvement for nutrient efficiency in the roots of leguminous crops in adaptation to acidic soils, and the interactions between roots and rhizo-microorganisms to improve crop nutrient efficiency and soil health. Furthermore, we overviewed the ecological benefits through intercropping nutrient-efficient soybean varieties with maize and tea plants, and thereby provided the theoretical basis and successful examples for genetic improvement of nutrient efficiency in legumes, and its application in sustainable agriculture systems.