The aim of this work was to study the responses of aerobic granulation process to antibiotics and investigate the antibiotics and antibiotic-resistant bacteria (ARB) removal and transport. Results showed that aerobic granular sludge (AGS) was dominant in the bioreactor at day 45, and the relatively high protein content from tightly bound extracellular polymeric substances (TB-EPS) facilitated aerobic granulation and maintained biomass stabilization. The protein contents in EPS and TB-EPS were positively correlated with relative hydrophobicity, thereby improving the adsorption capacity among hydrophobic particles. The chemical oxygen demand (COD), NH3-N, and total N removal efficiencies were 98.0%, 97.0%, and 92.4%, respectively. Five antibiotics, including kanamycin, tetracycline, ciprofloxacin, ampicillin, and erythromycin, were examined in piggery wastewater, with concentrations up to the concentration range of 29.4–44.1 µg/l, and the total antibiotics removal rate reached up to 88.4% ± 4.5%. A total of 5.2% of the total antibiotics were discharged from bioreactor, and 62.5% of the total antibiotics were degraded, and 32.3% of total antibiotics were adsorbed by aerobic granules. The presence of antibiotics rarely exhibited an influence on AGS formation, and the relatively high microbial activity of aerobic granules was beneficial to antibiotics removal. The ARB removal rate increased up to 89.4% ± 3.3%, but a large amount of ARB was enriched in aerobic granules.