Soil is vital for the production of food, the maintenance of environmental quality and ecosystem health. Soil is alive, and soil microorganisms (collectively called soil microbiome) are the driving force of elemental biogeochemical cycling and the bridge linking above- and below-ground ecosystem processes. Due to the limitations of conventional microbial research techniques, the majority of soil biological functions remain poorly understood and therefore untapped, rendering current research largely descriptive. However, in the last few years, new technologies, such as molecular biological approaches, bioinformatics and in situ imaging, have fundamentally changed views concerning the soil microbiome. The exploration of soil microbial diversity and its functions has become one of the frontiers of interdisciplinary science. The Chinese Academy of Sciences (CAS) initiated a strategic priority research program termed China Soil Microbiome Initiative (CSMI) in Beijing on June 4 of 2014. It aims to: (1) examine the diversity and biogeographical patterns of soil microbiome in the main terrestrial ecosystems in China; (2) elucidate the microbial ecology of the biogeochemistry of key elements; (3) characterize the interactions between above- and below-ground processes; (4) network research platforms for soil biological functions and their exploration; and (5) develop new technologies and methodologies for soil microbiome studies. It is expected that CSMI will bring significant breakthroughs in characterizing soil microbial systems and their functions in diverse Chinese soils, and will lay solid foundations for the exploration of the key roles of soil microbiome in ensuring food security and environmental quality. It is also envisaged that the implementation of the program will train new talents in soil biology research, will gain international recognition to facilitate closer collaborations, and will ensure advances into the future, not only for China, but also for the world.