Multilayer cage-houses for broiler rearing have been widely used in intensive Chinese farming in the last decade. This study investigated the characteristics and influencing factors of bacterial communities in the PM2.5 of broiler cage-houses. The PM2.5 samples and environmental variables were collected inside and outside of three parallel broiler houses at the early, middle, and late rearing stages; broiler manure was also gathered simultaneously. The bacterial 16S rRNA sequencing results indicated that indoor bacterial communities were different from the outdoor atmosphere and manure. Furthermore, the variations in airborne bacterial composition and structure were highly influenced by the environmental control variables at different growth stages. The db-RDA results showed that temperature and wind speed, which were artificially modified according to managing the needs for broiler growth, were the main factors affecting the diversity of dominant taxa. Indoor airborne and manurial samples shared numerous common genera, which contained high abundances of manure-origin bacteria. Additionally, the airborne bacterial community tended to stabilize in the middle and late stages, but the population of potentially pathogenic bacteria grew gradually. Overall, this study enhances the understanding of airborne bacteria variations and highlighted the potential role of environmental control measures in intensive farming.