The influence of temperature on the nitrogen removal efficiency of a solid-phase denitrification (SPD) system with a denitrifying SL-205 strain as a bio-augmentation microorganism was investigated in this study. The nitrogen removal effectiveness of the bio-augmentation SPD system declined to 56% when the temperature dropped from 30 to 13 °C. A high-throughput sequencing and correlation analysis revealed that the most dominant genera were Diaphorobacter, Dechloromonas, Clostridium sensu stricto 7, Stenotrophomonas, Thermomomas, Cloacibacterium, Azonexus, and Thauera. Except for Stenotrophomonas, the majority of the prominent bacteria were significantly reduced at lower temperatures. Acidovrax, Azospira, and Cloacibacterium showed a substantial negative correlation with Diaphorobacter in terms of relative abundance. The findings of this study imply that the abundance of the bio-augmented genus diminishes with decreasing temperature, although it remains the most abundant denitrification genus. In addition, given the appropriate hydraulic retention time, a bio-augmentation denitrification system can effectively treat wastewater at low temperatures. These findings can be used to estimate the SPD design parameters and determine the optimal operation approach. These findings provide a theoretical foundation for the bio-augmentation of SPD systems operating at low temperatures.