In this study, the effect of feeding with polymers on aerobic granular sludge (AGS) formation and stability was comprehensively investigated during 235-day operation. Results showed that the granules developed in starch-fed reactor possessed fluffy surface with overgrowth of granule size, and 60 % flocs were produced in protein-fed reactor, identifying feeding with polymers deteriorated AGS development and stability. Moreover, substrate conversion analysis revealed that ∼ 14 % of the consumed COD was recovered as storage of poly-hydroxybutyrate in polymer-fed reactor, much lower than 63.7 % in acetate-fed reactor. Extended Derjaguin-Landau-Verwey-Overbeek theory analysis showed that feeding with polymers increased the cell-cell energy barriers to 307.8 ∼ 388.8 kT, weakening the microbial aggregation capacity in AGS system. Microbial population results found that the relative abundance of Candidatus_Competibacter in protein- and starch-fed reactor displayed 0.01 ∼ 6.1 % and 0.07 ∼ 3.7 %, much lower than 81 % in acetate-fed reactor. Assembly mechanism analysis demonstrated that feeding with polymers enhanced the stochastic selection in shaping microbial assembly.