Carbon cycle is among the most important biogeochemical cycles in ecosystems, and microorganisms play critical roles in lots of its primary processes, such as carbon fixation, methane metabolism and carbon degradation. With the deep insight into functions of microbes in carbon cycle, we could better understand how they response and regulate the global climate change, which is a hot spot in the studies of microbial ecology. Previous studies focused on microbial isolations and cultivations, however, only little of the microorganisms in nature are cultivable while a majority of microorganisms are uncultured. With rapid development of the metagenomics technology, in-situ and comprehensive investigation of microbial functions and structures became feasible. In this article, we briefly introduced several widely-applied metagenomics technology such as quantitative PCR, DNA fingerprinting, microarray, clone library and high-throughput sequencing. Furthermore, we reviewed the advanced studies by using metagenomic methods to investigate the key functional genes involving in carbon cycle, including carbon fixation, methanogenesis, methane oxidation and carbon degradation. Finally, we prospected the future studies of the microbial metagenomics in carbon cycle.