Aerobic granular sludge process as a promising biotechnology has been one of the research hotspots in the area of wastewater treatment during the last two decades. In our study, after around 60 days' operation, filamentous granular sludge (FGS) was formed under low aeration (SAV = 0.085 cm/s) and multi-feeding conditions. The characteristics of FGS and the performance of the FGS system for organic matter and nutrients removal were investigated. The results showed that chemical oxygen demand (COD) and total organic carbon (TOC) removal efficiencies were relatively stable, while COD removal efficiency increased from 82% to 94% in the presence of sulfamethoxazole (SMZ) at low concentration (1 mg/L). At the same time, the TP removal efficiency could be improved and maintained at around 75%, while TN removal efficiency was flocculated at around 50%. The analysis of microbial diversity showed that Thiothrix and Trichococcus as typical filamentous species were detected and dominant in the FGS system. The abundance of Thiothrix increased from 15% to 34%, while Trichococcus decreased from 23% to 3% in the presence of SMZ.