Biological wastewater treatment systems are driven by microbial physiological processes, metaomics approaches obtain information from different molecular levels, providing a new way to understand microorganism in wastewater treatment systems. In this review, we summarize the developments of metaomics such as metagenomics, metatranscriptomics, metaproteomics and metabolomics, highlight the current research of metaomics and integrated metaomics in wastewaters treatment systems, also indicate the prospect in practical application.