In order to investigate the enhancement mechanism of modified three-dimensional elastic filler (MTEF) on the nitrogen removal performance of the integrated fixed-film activated sludge (IFAS) process, and to clarify the interactions between competition and synergy between activated sludge and biofilm in the IFAS system, an IFAS reactor (T2) filled with MTEF was employed for the study, while a sequencing batch reactor activated sludge process (SBR) reactor (T1) was utilized for comparison. IFAS and SBR reactors were operated over an extended period at ambient temperature to assess the enhancement of pollutant removal performance with the addition of the filler to investigate the competitive dynamics between activated sludge and biofilm under varying influent water qualities (C/N, N/P, and organic loading), and to analyze the synergistic relationship between activated sludge and biofilm at the microbial level using high-throughput sequencing technology. The results demonstrate that throughout the entire operational phase, reactor T2 exhibited superior pollutant removal efficiency. Compared to reactor T1, reactor T2 achieved an average increase in the removal rates of COD, ammonia nitrogen, and total nitrogen by 13.07%, 12.26%, and 28.96%, respectively. The findings on the competitive dynamics between activated sludge and biofilm indicate that the nitrification volumetric load of the IFAS system is significantly higher than that of a pure activated sludge system, suggesting that the IFAS system possesses enhanced nitrification capabilities. Furthermore, when dealing with wastewater characterized by low C/N ratios and high phosphorus pollution, or under substantial organic loads, the biofilm holds a competitive edge and the IFAS system exhibits improved stability. High-throughput sequencing data reveal that the microbial community structures in activated sludge and biofilm can influence each other, thereby enabling the IFAS system to effectively enrich denitrification-related functional microbial populations. Additionally, the biofilm has a certain enhancing effect on the expression levels of nitrogen metabolism-related functional genes in the activated sludge phase microorganisms, indicating that, in addition to competitive interactions, there is also a synergistic effect between the biofilm and activated sludge.