This study investigated the nitrogen transformation rates of different nitrogen-loading (20, 30, and 50 mg TN/L) biochar packed reactors (C:N:P = 100:5:1) within 125 days at 5 °C. The results showed that high nitrogen loading resulted in an NH4+ (TN) removal efficiency decline from 98% (57%) to 83% (29%), with biochar yielding a higher NH4+, TN and DON removal rate than conventional activated sludge. Moreover, all biochar packed reactors realized a quick start-up by dropping in temperature stage by stage, and the effluent dissolved organic nitrogen (DON) concentrations of R20, R30, and R50 were 0.44 ± 0.18, 0.85 ± 0.35, and 0.66 ± 0.26 mg/L, respectively. The nirS/amoA, nxrA/amoA, and amoA/(narG + napA) were deemed to be the markers of ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR), and specific nitrate reduction rate (SNRR), respectively. Compared with functional gene quantity data, transcription data (mRNA) introduced into stepwise regression analyses agreed well with nitrogen transformation rates. High nitrogen loading also resulted in the cell viability decreased in R50. Nitrogen loadings and operation time both led to a significant variation in cell membrane composition, and unsaturated fatty acids (UFAs) significantly increased in R30 (46.49%) and R50 (36.34%). High-throughput sequencing revealed that nitrogen loadings increased the abundance of nitrifying bacteria (e.g., Nitrospira) and reduced the abundance of denitrifying bacteria (e.g., Nakamurella, Thermomonas, and Zoogloea) through linear discriminant analysis (LDA).