Extracellular polymeric substances (EPS) of activated sludge are a mixture of high molecular weight polymers secreted by microorganisms, which have the double structure of tightly-bound EPS (TB-EPS) in inner layer and loosely-bound EPS (LB-EPS) in outer layer. The characteristic of LB- and TB-EPS were different, which would affect their adsorption of antibiotics. However, the adsorption process of antibiotics on LB- and TB-EPS was still unclear yet. Therefore, in this work, the roles of LB-EPS and TB-EPS in adsorption of a typical antibiotic-trimethoprim (TMP) at environmentally relevant concentration (25.0 μg/L) were investigated. The results showed the content of TB-EPS was higher than that of LB-EPS, which was 17.08 and 10.36 mg/g VSS, respectively. The adsorption capacity of raw, LB-EPS extracted and both LB- and TB-EPS extracted activated sludges for TMP were 5.31, 4.65 and 9.51 μg/g VSS, respectively, which indicated LB-EPS had positive effect on TMP removal, while TB-EPS had negative effect. The adsorption process can be well described by a pseudo-second-order kinetic model (R2 > 0.980). The ratio of different functional groups was calculated and the CO and C-O bond might be responsible for the adsorption capacity difference between LB- and TB-EPS. The fluorescence quenching results indicated that tryptophan protein-like substances in LB-EPS provided more binding sites (n = 0.36) than that of tryptophan amino acid in TB-EPS (n = 0.1). Furthermore, the extend DLVO results also demonstrated that LB-EPS promoted the adsorption of TMP, while TB-EPS inhibited the process. We hope the results of this study were helpful for understanding the fate of antibiotics in wastewater treatment systems.