The removal of 26 organic micropollutants (OMPs) in synthetic municipal wastewater was investigated via the process of aerobic sequential batch reactor (SBR) alone and SBR followed by nanofiltration (NF). SBR-NF performed better than SBR alone, ascribed to the contribution of NF: 1) complete biomass rejection resulted in diverse microbial community and much less fluctuated performance than SBR alone, and 2) direct OMPs rejection (74–98%) increased their retention time in SBR and thus overall removal via biodegradation/transformation and accumulation in SBR. Nine OMPs showed high biological removal (over 60%), 6 OMPs showed moderate biological removal (30–70%) and 10 OMPs showed low biological removal (below 40%). Most readily and moderately biodegradable OMPs contained strong electron donating group. Most refractory OMPs contained strong electron withdrawing group and/or halogen substitute. The batch addition of powdered activated carbon (100 mg/L) into SBR showed short term sorption performance for both OMPs and bulk organics.