In response to the often violent and dynamic changes in the immediate environments, microbes self-adjust extracellular polymeric substances (EPS) excretion and form aggregates, a stabilizing substantial life form, for survive and ecological functioning. Notwithstanding the importance of microbial EPS on practical functioning of activated sludge systems, mechanistic understanding of the role of EPS on microbial clusters formation remains elusive. We investigated EPS production at resources allocation, in terms of dissolved oxygen, carbon and nitrogen resources-limitation, and impacts on microbial clusters formation of activated sludge system. Results showed that microbes experienced sluggish clustering and formed small size clusters inhabiting sufficient resources environments, while relatively larger size clusters were observed at limited resources conditions, consistent with available observations. Interestingly, we found a negative correlation between EPS contents and yielded microbial cluster size. Quantitative estimations of clusters surface charges revealed that lowing EPS contents were perfectly correlated to decayed surface negative charges, which yielded lower energy barrier that facilitates cell–cell and cell–clusters collisions essential for efficient microbial aggregation and thereby, favors larger sizes clusters formation. These results offer new insights into microbial clustering dynamics of activated sludge system, and are of important practical guiding for efficient functioning of biological wastewater treatment processes.