Nitrogen (N) remains a great challenge in wastewater treatment while attempts to remove N has continuously been a research point for decades. In this study, the long-term performance of four identical-shape denitrification MBBRs (moving bed biofilm reactors) with four different configurations of cylindrical polyethylene as carriers (Φ25 × 12, Φ25 × 4, Φ15 × 15, and Φ10 × 7 mm) for advanced N removal of real reverse osmosis concentrate was investigated in great detail. The N of the real concentrate can be effectively removed by denitrification MBBRs when the pH, temperature, hydraulic retention time (HRT), C/N ratio, and filling rate are 7.50–8.10, 24~26 °C, 12 hours, 6.6, and 50%, respectively. The results showed that the MBBR with the Φ15 × 15 poly-carrier had the best removal efficiency on NO3-–N (78.0 ± 15.8%), NO2-–N (43.79 ± 9.30%), NH4+–N (55.56 ± 22.28%), and TN (68.9 ± 12.4%). The highest biomass of 2.13 mg/g-carrier was in the Φ15 × 15 poly-carrier was compared with the other three carriers, while the genes of the Φ15 × 15 poly-carrier reactor were also the most abundant. Proteobacteria was the most abundant phylum in the system followed by Bacteroidetes and then Firmicutes. The entire experiment with various parameter examination supported that Φ15 × 15 poly-carrier MBBR was a promising system for N removal in high strength concentrate. Despite the lab-scale trial, the successful treatment of high strength real reverse osmosis concentrate demonstrated the reality of the treated effluent as possible reclaimed water, thus providing a good showcase of N-rich reverse osmosis concentrate purification in practical application.