The development of high-throughput sequencing technology promoted the wide applications of omics in the study of environmental microbiology. Among all omics technologies, metagenomics is the most critical and widely used method at present, while bioinformatics plays a very important role in its applications. The bioinformatic technologies were involved in metagenomics data collection, storage, preprocess and analysis. Therefore, it is not only the key of metagenomic development, but also the bottleneck for its implementation. This paper introduces the commonly used bioinformatic pipelines in both shotgun metagenome and amplicon of high-throughput sequencing. In next few years, the decline in cost and the increase in depth of high-throughput sequencing will dramatically elevate the difficulty on the analysis of metagenomic data. It is imperative to pay more and more attentions to develop the bioinformatics tools and analysis pipelines. Nowadays, we should strengthen the construction of fundamental analysis and storage platform to facilitate the data mining for ordinary microbial researchers. Meanwhile, we should develop more bioinformatic algorithms and tools to overcome the current bottleneck in the analysis of metagenomics.