To study the removal performance of a constructed rapid infiltration (CRI) system and its microbial community characteristics, we took the demonstration project of a CRI system that has successfully operated for 15 years as an example, aiming to analyze the CRI system’s removal performances for COD, NH₄⁺-N, TN and TP. Meanwhile, high-throughput sequencing technology was used for the first time to study the microbial community diversity and structure in the CRI system. The results showed that the average removal efficiencies for COD and NH₄⁺-N were 75.52% and 92.94%, and the average removal efficiencies for TN and TP were respectively 39.74% and 42.78%. High-throughput sequencing technology indicated that a variety of bacterial phyla were found in CRI’s bacterial communities, including Bacteroidetes, Actinobacteria and Acidobacteria, among which Proteobacteria dominated. At the genus level, a spatial variation was illustrated for the diversity and structure of bacterial communities. The dominant genera on the surface layer (0 cm) of CRI were mainly Nocardioides, Sphingomonas, Bryobacter and other microorganisms that can degrade organic matter, and the dominant genera in the inside (30-120 cm) were mainly microorganisms that play an important role in removing nitrogen. This study provided a theoretical basis for the long-term operation of a CRI system.