The information of microbial genomics is accumulated with the progress of pure culture and metagenome research. Metaproteomic study will contribute to our understanding of genomic function. Recently, metaproteomic study of microbial community is becoming an effective approach to understand the function of microbial ecology in post-genome era. In this review, the new metaproteomic approach was introduced, including extraction and identification of metaproteomes and application in microbial ecology. Finally, the future perspectives were discussed.