The lab-scale aerobic granules process was applied for low carbon to nitrogen (C/N < 4) wastewater treatment under different hydrodynamic shear forces. Results revealed that aerobic granules exhibited strong adaptability and stability. The aerobic granules might adopt an extracellular polymeric substances (EPS) regulating mechanism to address the changes in operational conditions, especially through growing secretion of fluorescence protein. The hydrodynamic shear force determinedly shaped and regulated the diversity and structure of dominant microbial community, briefly, reduced aeration intensity with increased time led to higher microbial richness, lower diversity and evenness, and shifts of predominant microorganisms. Phylogenetic classification of the key functional groups including bacteria related to carbon and nutrients removal, EPS production and quorum sensing (QS) presented much more differences among the reactors subject to different conditions. Therefore, the present work adds insight into the comprehensive understanding of the effect of aeration induced hydrodynamic shear force on aerobic granules.