This study characterizes the extracellular polymeric substances and bacterial community composition of aerobic granules exposed to cefalexin (CLX). The presence of CLX potentially decreases granular stabilities, resulting in a lowered granule diameter. Chemical oxygen demand and NH4+–N removal efficiencies were slightly decreased and the denitrification process was inhibited with CLX addition. Extracellular polymeric substance contents were significantly increased in aerobic granules exposed to CLX. The shifts of fluorescence intensities and peak locations in 3D-EEM fluorescence spectra indicated changes of EPS components. High-throughput sequencing analysis showed aerobic granules with CLX addition in synthetic wastewater had superior diversity of microbial species, and this was the reason that the level and components of EPS changed. The species richness for bacteria was increased from 341 to 352, which was revealed by Chao1. The Shannon index of diversity rose slightly from 3.59 to 3.73 with CLX addition. The abundance of Proteobacteria significantly decreased, while the abundance of Bacteroidetes and Chloroflexi underwent a highly significant increase in aerobic granules exposed to CLX.