Improving nitrogen removal is a significant concern in the biological treatment of ammonium nitrogen (NH4+-N) wastewater with low chemical oxygen demand (COD)/NH4+-N (C/N) ratio, and microorganisms are the critical factor affecting nitrogen removal. In this study, a laboratory-scale biological contact oxidation reactor (BCOR) system was successfully started up (day 1 to day 47) and stabilized (day 48 to day 320). A 16S rRNA gene sequencing analysis showed that the phyla Firmicutes and Bacteroidetes were first observed as the dominant microorganisms in the BCOR for the ammonium nitrogen wastewater treatment with a low C/N ratio. The genera Bacteroides (phylum Bacteroidetes), Porphyromonas (phylum Bacteroidetes), Dialister (phylum Firmicutes), and Anaerococcus (phylum Firmicutes) also became the main microorganisms in this system for the first time. These microbial communities enabled the system to achieve an average ammonium nitrogen removal efficiency and total nitrogen removal efficiency of 95.8 % and 88.1 %, respectively, during the operational period. It indicated that these dominant microorganisms in the BCOR system played an essential role in improving the performance of biological nitrogen removal. This conclusion will play a critical role in promoting the microbial mechanism research and technology engineering application of the BCOR system for treating ammonium nitrogen wastewater with a low C/N ratio.