Advances in high-throughput sequencing have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field metagenomics, which is often defined as the analysis of DNA sequences from microbial communities in environmental samples without prior need for culturing. Microbiome data management and analysis have caused concern for microbial researchers because of the dramatic increase of metagenomics data. It has been a research hotspot that how to mine valuable information for further application form such big microbial data. Till now, many metagenomics computational tools and databases have been provided in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and international microbiome projects as well as the platforms for microbial data archiving and analysis, such as Human Microbiome Project (HMP), Earth Microbiome Project (EMP), Metagenomics of Human Intestinal Tract (MetaHIT), MG-RAST, iMicrobe, Integration Microbial Genomes (IMG) and EBI Metagenomics and so on. We also discussed about the basic pipelines and main tools for metagenomics data. Finally, we proposed the necessity of establishing a platform for multi-source microbial data management and bioinformatic analysis.