Activated sludge is the most popular artificial ecosystem for biotechnological wastewater treatment worldwide, and microorganisms are the key driver of its de-contamination ability of wastewater. The study of all species and genes of activated sludge microbial communities (referred to as ‘microbiome’) has undergone three major stages of tremendous development: microscopic observation and pure culture isolation (since 1915), PCR amplification and sequencing (since 1994), and high-throughput sequencing (HTS) and meta-omics (since 2006). Correspondingly, our understanding of the activated sludge microbiome has experienced the leap from the earliest observations of the morphology of micro-fauna (e.g. Vorticella and Rotifera) and other microorganisms to complete diversity profile of the entire microbiome nowadays. In the past 13 years, HTS-based meta-omics research has been widely used to reveal the structure and function of activated sludge microbiome. We have now fully realized that the activated sludge microbiome contains a large diversity of uncultivable new species and genes, driving the degradation and conversion of various pollutants. At present, amplicon sequencing analysis of specific molecular marker genes has been widely used to reveal the spatial and temporal diversity of urban and industrial wastewater treatment activated sludge microbiome, typical functional bacteria (e.g. nitrifying bacteria and polyphosphate-accumulating bacteria) and community assembly patterns, providing theoretical basis for achieving precise regulation of activated sludge microbiome functioning. Metagenomic studies have comprehensively revealed, the microbiome-driven carbon, nitrogen and phosphorus cycling in activated sludge and the biodegradation and transformation mechanisms of organic micro-pollutants at levels of community, population and individual genomes. Future research on the activated sludge microbiome is supposed to make breakthroughs in the following four technical aspects for the achievement of precision eco-genomics: i) standardized meta-omics approaches and absolute quantification, ii) high-throughput culture omics; iii) high-throughput functional metagenomics, and iv) integrated use of multi-omics methods and multiple methods, which are important for maximizing the ecological and engineering values of activated sludge microbiome in wastewater treatment and resource recovery.