Soil microorganisms are a driving force in material recycling and nutrient transformation in soil. However, for a long time, soil has been treated as a “black box” system, wherein microbial diversity and biochemical processes they participate in soil remain to be explored. Since most of the soil microorganisms are still quite hard to be isolated for culture, traditional culture methods are quite limited in helping reveal compositions and functions of soil microbial communities. The metagenomic method is able to explore the structures and functions (sequence-driven approach) of soil microbial community and to screen bioactive materials and new genes (function-driven approach) through extracting all microbial DNAs direct from environment samples and then sequencing or constructing clone library, thus breaking through the bottleneck of the traditional methods and greatly enriching the knowledge about soil microbial biodiversity and functions. While reviewing main procedures of the metagenomic technique, the paper focuses on the introduction to application of the next-generation sequencing (NGS) technologies in metagenomic research and processing of the huge volume of data it may produce. The new processes on soil microbial ecology with the metagenomic technique is then discussed. And in the end, the authors propose that research projects on soil metagenomics projects should be launched at the national level to explore soil microorganism communities and their variation, so as to contribute to the causes of bioresource exploitation, agricultural production and environment protection.