The implementation of latest International Maritime Organization (IMO) emission standard has raised stringent nitrogen requirements for marine domestic sewage discharge. In order to meet new discharge standards, novel aerobic-anaerobic micro-sludge membrane bioreactor (O-AMSMBR) for chemical oxygen demand (COD) and total nitrogen (TN) removal from ship sewage is proposed. Results indicated that novel MBR achieved better COD and TN removal efficiency (R-avg(COD) = 91.6% and R-avg(TN) = 88.07%). The amount of anaerobic sludge in O-AMSMBR was reduced by 80% however TN removal rate was 10% higher than traditional Membrane Bio-Reactors (MBRs) technology. Based on the analysis of sludge characteristics, high TN removal efficiency is achieved via collective role of simultaneous nitrification and denitrification (SND) and "anaerobic micro-sludge effect". Microbial community analysis also revealed that Rhodobacter and Pseudomonas are dominant species in anaerobic zone, which has a direct relationship with "anaerobic micro-sludge effect". Further, transmembrane Pressure (TMP) showed that "anaerobic micro-sludge effect" not only has a positive effect on pollutants removal but also can suspend membrane fouling. The outcomes of this study suggest that post-anaerobic integrated with micro-sludge methods played a vital role in keeping good pollutant degradation in ship wastewater treatment. The presented results can provide new insights into ship sewage treatment by MBR technology.