Abstract <p>In this study, actual piggery wastewater was utilized to cultivate aerobic granular sludge (AGS), which was used to remove conventional and heavy metal pollutants from piggery wastewater. The removal mechanism of Cu²⁺ and Zn²⁺ by AGS was investigated using adsorption and high-throughput sequencing methods. The results showed that the extracellular polymeric substance (EPS) components and dominant bacterial species in AGS play important roles in the removal of Cu²⁺ and Zn²⁺. Both dynamic and static factors influence the abundance of microorganisms, which consequently affect the Zn²⁺ adsorption effect of AGS. Microorganisms that are adapted to the presence of heavy metals and possess competitive advantages contribute to the adsorption of Cu²⁺ and Zn²⁺ by AGS. There are positive and negative correlations within the microbial community after AGS adsorption of Cu²⁺ and Zn²⁺. The results of this study are of great significance for promoting the widespread application of AGS technology.</p> Key points <p>•&#xa0;<i>The removal of Cu</i>^<i>2+</i><i> and Zn</i>^<i>2+</i><i> mainly depends on the EPS components in AGS</i></p> <p>•&#xa0;<i>The biological activity of AGS has a significant impact on the adsorption of Zn</i>^<i>2+</i></p> <p>•&#xa0;<i>Dominant microorganisms play an important role in the adsorption of heavy metals</i></p>