The integrated effects of temperature and COD/N ratio on performance, biofilm characteristics and microbial community in up-flow anaerobic filter-biological aerated filters (UAF-BAFs) were investigated. Results indicated that the UAF-BAF system could achieve excellent COD, NH-N and TN removal, in which effluent quality well met the Class 1A standard. Biofilm physicochemical characteristics showed that the biomass, biofilm thickness and extracellular polymeric substance (EPS) content in the UAF-BAFs reduced with the decrease in COD/N ratio, but were enhanced under low temperature. The biofilm structure characterized by CLSM in the UAF-BAFs significantly shifted, which was closely correlated with operational conditions. Sequencing analysis revealed that Proteobacteria, Epsilonbacteraeota, Bacteroidetes and Firmicutes were dominant in the UAFs and the abundance of ammonium oxidizing bacteria (AOB) was responsible for nitrification performance in the BAFs. Functions analysis indicated that amino acid metabolism, carbohydrate metabolism, energy metabolism and lipid metabolism were clearly regulated by parameters changes.