Removal of nitrogen compound in wastewater has been successfully developed with various activated sludge based processes. The microorganism immobilized on media enhanced biological efficiency by increase in biomass concentration, however the microbial community composition in the media was little revealed. A modified Ludzack-Ettinger (MLE) process was operated with immobilized media with polyvinyl alcohol and polyethylene glycol. MLSS in aerobic reactor was maintained at 50,000 mg/L and 40,000 mg/L in anoxic reactor by the media. 99% of ammonium in influent was oxidized but organic nitrogen resulted from microbial growth reduced total oxidation rate during the operation. Nitrate reduction rate increased by the addition of glucose for C/N ratio adjustment to 4.5. Based on total nitrogen concentration, the removal efficiency of nitrogen was 48.2% after C/N ratio adjustment, which showed the mid-range of nitrogen removal efficiency in MLE. Microbial community composition was compared between aerobic and anoxic media by NGS technique with V3-V4 region of 16S rRNA gene. Proteobacteria was the dominant phylum both in aerobic and anoxic media, and the ratio was 39.7% in aerobic media and 65.9% in anoxic media. Bacteroidetes was secondly largest phylum. The dominant genera in aerobic media were Nitrospira and Povalibacter. Ratio of nitrification-related genera was 45%. On the contrary, the dominant genera in anoxic media were Desulfomicrobium, Desulfobulbus, and Methyloversatilis in sequence of dominance. Total genera related with denitrification, including Dechloromonas and Flavobacterium amounted 63%. Population of microorganisms in each reactor was compared in terms of diversity by QIIME 2 algorithm. The Chao1 index values of α-diversity were 606.05 and 415.53 for aerobic and anoxic media, respectively, which showed higher population diversity in aerobic media than in anoxic. The microbiological community on the immobilized aerobic and anoxic media would help future microbial studies in wastewater treatment process.