Partial nitritation (PN) and the anaerobic ammonium oxidation (ANAMMOX) process provides a novel method to solve the problem of low TN removal efficiency in a constructed rapid infiltration (CRI) system, and PN is the prerequisite to realize the process. In this study, the feasibility of achieving PN in a CRI system by synergistic regulation of free chlorine, filter height and influent pH was investigated. The characteristics of microbial community structure during the stable operation of the PN process were also discussed. The results showed that after adding 3 mg/L of free chlorine continuously for 23 days, adjusting the effluent filter height to 75 cm and the influent pH to 8.2~8.5, the PN process successfully started with the NO₂^--N accumulation rate staying stable at about 90% and effluent NO₂^--N/NH₄⁺-N ratio between 1.23 and 1.35, thus providing suitable influent conditions for the subsequent ANAMMOX. Based on 16S rRNA high-throughput sequencing, a total of 41 phyla, 144 classes and 310 genera were detected from the stable running PN-CRI system. The detected ammonia-oxidizing microorganisms mainly included Nitrosomonas, Nitrosovibrio and Candidatus Nitrososphaera; while only Nitrospira was detected in nitrite-oxidizing bacteria genera with its relative abundance at only 6.7~10.0% of the total abundance of ammonia-oxidizing microorganisms. This indicated that the synergistic regulation strategy could selectively eliminate nitrite-oxidizing bacteria, thus creating favorable conditions for the occurrence of PN. These findings could provide a theoretical basis and scientific reference for efficient and economical nitrogen removal in a CRI system.