The impact of a novel sawdust-modified carrier on the performance of aerobic sequencing batch reactor (SBR) was examined. Compared with the conventional polyethylene (PE) carrier, the sawdust-modified carrier had coarse surface and porous side wall, which was beneficial for the rapid formation of biofilm. The biomass of sawdust-modified carrier was 3.4 ± 0.7 times more than those of PE carrier at the end of this study. The biofilm gotten from suspended carrier had higher extracellular polymeric substances (EPS) concentrations than activated sludge (AS). The EPS from biofilm contained higher proportions of polysaccharides compared to those from AS. The SBR with addition of sawdust-modified carrier exhibited higher ammonia nitrogen removal efficiency (84.8%) than the one with addition of conventional PE carrier (73.1%) in a typical cycle at 12 h. The volumetric nitrification rates of modified carrier were higher than those of conventional PE carrier. High throughput sequencing revealed that sawdust-modified carriers exhibited greater microbial richness and diversity compared with traditional PE carriers. Saccharimonadales was the most predominant genus that removed organic matter under aerobic condition, whereas Nitrospira was the dominant nitrifying genus. The present study verifies the advantage of sawdust-modified carrier, which has the potential for the full-scale application in the future.